I don't know JustinOther's reasons for SKSE/non-SKSE versions or options within scripts, but I have two reasons:

1) I started using Script Extenders back in the Morrowind days when they were buggier and had conflicts, so I know people's concerns about running third-party programs with the game aren't completely crazy. I was an early adopter of MWSE but was still somewhat reluctant to use it. And MWSE did have problems, especially because in the early days you really couldn't run it and MWE (Morrowind Enhanced) together. (MWE also added new script abilities to the game, so we had two somewhat incompatible programs and MWE was already established before MWSE come on the scene.) Making a version of a mod that didn't require MWSE really was the right thing to do. OBSE was technically far superior to anything we tried with MWSE and SKSE is even better so the technical issues aren't a problem, but collective wisdom hasn't forgotten old lessons yet.

2) I'm impatient. When I make a mod I'm almost always trying to do something unusual before there's a Script Extender function to make my life easy. So I end up creating a functional, but incomplete or annoying version of what I really wanted using only the game's original features. Then the OBSE/SKSE team creates the function I need and I can rebuild a better version (or sometimes just fix the original scripts) to get the mod I really wanted. At that point, it's really not any extra work to release both and it makes some people happy to use my first draft version. Of course, I also don't release all of the mods I create simply because it would be too much hassle to make them presentable.

JustinOther is obviously a skilled programmer and may not have stopped to consider that "Scripts can easily accommodate both" doesn't always translate into "Modders can easily accommodate both" for the less experienced modders.

I think it's a cultural difference. Do you attempt to mod every other game you play? Are people who are seriously into TES as interested in other, less flexible games? The existence of developer-provided modding tools attracts the kind of audience that is interested in modding, that's less willing to accept the game for what it is. If you're willing to go beyond the content that the original developers provide, then you're probably more likely to go beyond the tools they provide as well.

When modding, there's a point at which you're no longer playing the original game. Most people aren't interested in crossing that line. For the rest of the gaming population, which TES has progressively attracted as it's become more available and approachable, modding the game is a novelty. They're more likely doing it for convenience, or to fix minor annoyances, than with the intent of reshaping the whole game. It's not a creative platform for them. They just want to play the game, for enjoyment, not devote a lot of time learning a bunch of tools.

To some of you, the things a script extender makes possible may seem essential, or like things players would obviously want. But some players simply don't want those things, don't feel they make the game any better. Some people are happy with the game as they got it. Some just want to make minor changes. Some want to fundamentally change everything about it. There's a broad range of people a TES game appeals to, and they don't all want the same things out of it. People across the spectrum just need to respect that.

For some of you, a TES game isn't just a game. It's practically a lifestyle. The time necessary to research all the tools, install everything, research mods, create mods, resolve conflicts, etc. is all worth it to you. And that's fine. But some people seem to get really snobbish about it, acting as if anyone not willing to put so much time and effort in doesn't deserve to play the game at all. That kind of attitude is what drives people away. The violently pro-SKSE attitude creates the equally violently anti-SKSE attitude.

Can't say I've ever seen anyone being violently pro-SKSE before. Only the violently anti-SKSE side.

That said, we're still in Skyrim's early period. When Skyrim is 7 years old (as Oblivion is now) I'm pretty certain you'll be hard pressed to find anyone who doesn't have SKSE installed. That will simply grow naturally with time. Nobody is going to need to forcefully advocate for that.

Once again, a cultural difference. The kind of people likely to still be playing Skyrim once it's 7 years old are the same kind of people who would be willing to use SKSE in the first place. It's not necessarily that the SKSE userbase will grow so much as it is that the rest of the userbase will fall away.

I've seen a few "Of course you should use it. What are you afraid of idiot?" type comments about SKSE. Although just a few and not quite that blunt. But it was pretty clear that was the thought behind what was written. There were more of those back in the Morrowind days and I still remember some PM discussions trying to get the over-zealous MWSE supporters to stop doing that.

Pro-SKSE is a bi-product of anti-SKSE. There's no need for pro if there isn't an anti.

I don't think so. I've seen a lot of anti-scriptextender rants and helped a lot of people instal and use the scriptextenders and in my experience you have three main groups in this crowd:

First you have the people who don't want to use SKSE because it's not "official" and it's a spooky executable, so they're scared of it. I've seen similar reasoning for why some people don't want to use the unofficial patches. With these people I often wonder why the hell they're using mods in the first place if they're so scared of anything that isn't official". Granted, it's a good thing to not blindly trust any executable you download of the Internet. But when you have a lot of users telling you that it's safe and you can scan the thing yourself with all the virusscanners in the world and verify it's safe, it's probably okay to try that spooky executable.
If you have the patience you can gently explain that it's not virus, that they can do a scan themselves if they don't believe you and that it won't blow up their computer. Sometimes this works and sometimes they're entrenched in their castle of fear.

The second group are the people who think they're too cool for readmes. They download SKSE, unpack the archive, realise they have no clue how to instal it and completely ignore the reaadme. Bonus facepalm points if these people then proceed to whine on the Internet about how there are no instructions (if only there was readme).
Generally if you point out that they should read the readme, they see the instructions and get things sorted out. Sometimes these people lash out and react angrily when you point them towards the readme though. I can only assume that on some level they realize that not reading the readme was stupid and they're angry at you for making them realize that.

And the last group are the computer illiterates. These are the people who even if they manage to find the readme on their own, completely fail to comprehend the clear instructions written in basic English. I would understand it if there was a language barrier, but these people can often post on forums in English just fine.
The introduction of the Workshop and how it attempted to make installing mods a one-click affair, was a good idea for these people since they will obvious have trouble with any mod. Sadly, that approach just doesn't work for Skyrim.
To be honest, I don't there's much that can be done to help this group. The instructions in SKSE's readme are pretty darn simple. Heck, I've even seen someone screw up the installation when using the SKSE installer. No clue how he managed that.

I have not spotted any violently pro-SKSE attitude.
What I know do exist are people who know SKSE is not some dangerous virus and is not difficult to install, and who roll their eyes derisively at the people who whine about how dangerous and/or difficult to instal SKSE is. I'll confess that I myself have done that from time to time. It's not helpfull in anyway, but it's hard not to do when you http://steamcommunity.com/app/72850/discussions/0/810919057051768756/?l=dutch

Having worked with some people (some who aren't into gaming, some who are) who could be described as 'computer illiterate', I in fact have a lot of sympathy for them. I started out as a software engineer, working with people who were extremely computer literate. I assumed anyone could deal with the basics if they just concentrated. As time has gone on, I've increasingly come to realise that very intelligent people can simply have no aptitude for absorbing the (to them) arbitrary and unfathomable instructions for any kind of software installations. Quite simply, being technically minded is a skill that can be learned, but it is much, much harder to learn it if one doesn't have the aptitude - and some people are sensible enough to know their limits and not try to tackle something they reckon they have a good chance of mucking up.

These are the people who'll never install SKSE, or BOSS, or NMM, and who hope (probably wrongly) that the Steam Workshop's one-click subscribe is the way they can improve their game without wrecking it.

I have far more patience with these people that with the people who think they know everything and can't be bothered to Read The [censored] Manual .