I tend to fall into the COMPLEX camp, including some sub-divisions that aren't absolutely required. Then too, I use my Packages as combo install-packets / archives. If a mod's esp needs cleaning I generally make both it and the original esp separate selectable sub-folders thusly:
00 esp - original
00 esp - TES4edit cleaned
This makes much sense to me. Not only does it insure the original is not lost, but gives me a quick and easy way to convert back should the edited esp prove defective. For this same reason I keep both original and PyFFi meshes as selectable options:
01 meshes - original
01 meshes - PyFFI 219
That looks sensible. What I do with backups created when cleaning plugins (and I have a
lot of these) is store them all in a subdirectory under my mods storage directory. My BAIN packages only include the cleaned version. But I can see the point of your method. Just haven't had to use an "unclean" version, so far, so I suppose any advantage is moot anyway.
As for PyFFI, I am not quite certain I trust it. I would rather not sacrifice
any image quality, when I do not need to. Or does it not affect IQ
at all? I very much dislike ugly and overly simple meshes in particular, you see. But if I did use PyFFI, I might consider your approach, for that.
10 DistantLOD - ARCHIVE ONLY could easily be dispensed with since TES4LODgen renders it unnecessary and in any case few modern mods include DistantLOD (not be be confused with RAEVWD or distant Landscape LOD). If present I prefer to keep the files for completeness only, not for use.
I have simply selected "Skip DistantLOD" (along with a few other things) in Wrye Bash's installer tab. So I also keep them, even though I never install them. It seems we share the preference, to keep all files, regardless. I even keep old versions of mods, just in case!