Basically, his point was that if you're going to install a bunch of additional creatures and items, you're going to end up with a bunch of stuff in the game that isn't balanced with a vanilla setup. Therefore instead of trying to add a bunch of disparate stuff you're better of just going with an overhaul or something like MMM, since they're designed with balance in mind you won't have to worry about running into a creature that's impossible to beat or pick up a weapon that kills everything in a single hit.
My response was basically, "why assume the people making the various creature/item mods are incompetent?" I'm sure there are a number of mods on these lists that include creatures/items poorly balanced with the vanilla game. But I'm also sure that a lot of modders had balance in mind when creating their creatures/items, so adding them to the game will do nothing but expand the diversity of what you come across.
The whole motivation for these lists and compiling as many of these mods as possible is to make it easier for someone to add something simple to the game in a modular way. If you don't want to install a major overhaul that adds similar things, but want some extra types of wolves in your game, you can find a mod that does it. Maybe it will be balanced well, maybe it won't, but the option's there.
That being said it's not my intention compiling these lists to provide some kind of alternative to going the route of overhauls. I just happen to be playing a vanilla game, had collected a number of these mods for myself and to include on my mod website, and decided it'd be a good idea to be real thorough about it. Sure I may not be using any overhauls myself that add similar things, but that doesn't mean the spirit of the lists is like, "screw overhauls, you can just add some new creatures and items yourself without having to change anything else!" The latter sentiment in that statement is the intention though, giving the player the option to do things one-by-one if they like. But it's not meant to imply that overhauls aren't fun, just that some people might want to add little things sometimes.
Now back to watching random clips of The Wire on YouTube for six more hours!