To begin with, Mr. Human Bean adds no bash tags to his mega merge. Possible problem right there, doesn't seem Wrye Bash friendly (so this idea might be good with normal load orders, but nor Wrye Bash).
You have to be careful with the tags. Especially for Spell Tomes UOMP, in fact, I'm not sure it should be tagged. Mine isn't and it all seems to be working properly. You certainly don't want to be using things like Graphics and NoMerge on it in a mega package since that will then apply to the ENTIRE merged mod. See what I'm getting at?
The mods I wish to merge are as follows:
Unofficial Shivering Isles Patch.esp 1.4.0 {{BASH:C.Light,C.Owner,Invent,Names,Stats}}SM Plugin Refurbish ? SI.esp 1.11 DLC Horse Armor ? Unofficial Patch.esp 1.05 {{BASH:C.Light,C.Owner}}SM Plugin Refurbish ? HorseArmor.esp 1.11DLCOrrey ? Unofficial Patch.esp 1.0.3 {{BASH:C.Light}}SM Plugin Refurbish ? Orrey.esp 1.11DLCVileLair ? Unofficial Patch.esp 1.0.5 {{BASH:C.Light}}SM Plugin Refurbish ? Vile Lair.esp 1.11DLCMehrunesRazor ? Unofficial Patch.esp 1.0.4 {{BASH:C.Light,Relev}}SM Plugin Refurbish ? MehrunesRazor.esp 1.11DLCThievesDen ? Unofficial Patch.esp 1.0.5 {{BASH:C.Light,Relev}}DLCThievesDen ? Unofficial Patch.esp 1.0.4 {{BASH:C.Light}}SM Plugin Refurbish ? Thieves Den 1.11DLCBattlehornCastle ? Unofficial Patch.esp 1.0.4 {{BASH:C.Light,C.Owner}}SM Plugin Refurbish ? Battlehorn.espKnights ? Unofficial Patch.esp 1.0.9 {{BASH:C.Light,Invent,Names,Relev,Stats}}
I notice that Gecko does not import tags into merged mods.
Nope. Tags are just description text and Gecko has no idea what they mean. It generally just uses the description from the first mod on the list, which would include any tags it has.
so Question (1)
If the final merged mod had all these tags ? is that harmful? I guess it would also mean that tags (releve,deleve) would be added to content such as the Orrey, which normally would not require those tags. I'd use Wrye Bash and tag it myself.
Well the Delev/Relev isn't something I'm completely sure on. But the Light and Climate ones should still be used as what they're trying to do will end up merged into the larger ESP and still need to be done. But it does come at the slight danger of causing plenty of other cells to pick up on the changes that otherwise may not need them.
Question (2) The above list does not include the:
DLCSpellTomes ? Unofficial Patch.esp 1.0.1 {{BASH:Graphics,NoMerge}} Which has a bash/no merge option ? is merging that into this mod (and not bash) OK?
Don't see why it had those tags, ever. You'd probably want to remove those.
Question (3) Nor does it include:
SM Plugin Refurbish ? Knights.esp 1.06 Which is a mergeable (into bash) mod ? would merging this into this mod be OK?
No, because once its contents are merged the larger file will have cell records and Bash won't merge those.
Question (4) Could Wrye's Knights patch: http://wrye.ufrealms.net/Knights%20Patch.html also be integrated? (is that patch even necessary anymore?)
Question (5) Could the Mystic Emporium Bug Fix: http://www.tesnexus.com/downloads/file.php?id=12745 also be merged ? even though, again, it is a normally merged into bash patch? (no real point to that other than being neat, I guess).
Both of those have been rendered obsolete by the current UOMPs. You don't need them at all.
Finally Question (6) recommended load order if the mod and the numerous tags are acceptable.
Well. Obviously it'll need to go after your DLCs, and those will need to all be in a block somewhere together, including Knigts.esp. The result may also require you to shuffle your DLC order around a bit. And you won't be able to allow BOSS to move Knights.esp around on you anymore.
This is also something that's going to mandate you be extra alert for bugs. I'd recommend backing up saves and proceeding with a test subject or other semi-throwaway save you can risk on it.