Gerax,
is good to see that you have experimented a lot with it and you have arrived to many interesting conclusions.
By the way (and this is just a personal preference), I consider that contents which are only loaded at the beginning of the Mission and not "pre-loaded" we would say, don't have any real need of being splitted. What I mean? The Maps could perfectly be in a single Files\Maps folder (kind of what you suggest), with only different all.ini files loaded through differnet MODS folders, to make only a sub-set of maps available in the corresponding case. Regarding sounds, PaintSchemes, etc., all will be shared and there's no problem, because they are used "on-demand" by the program.
As a general strategy I adopted a slightly different one of yours, but again: this is only a matter of taste. I have a clean UP2.01 Files folder with all the extra 3DO for cockpits, etc., plus all the maps I could gather, etc, etc. From there I have set up different MODS folders (here it's kind of your system), and everything special is loaded from there, ini files, general MODs, planes MODs, etc.
I was thinking apart of having the typical structure we have first loading Files and later loading MODS over it, to make a new version of the wrapper with this structure: Files / CoreMODS / MODS. I think that it will make loading clearer and will avoid some kind of troubles we typically have. For troubleshooting it will be good too.
Regards,
Pablo