If you installed the modpack on a game in progress then it could possibly change some in-game player colors, bypassing the in-game check I was talking about that may change the color of the civ in the game because I THINK IIRC that check only takes place when the player initiates into the game. It's possible then changing the xml color on a civ later might reset that color in play and allow for such duplicates to exist in play.
The biggest WTH comes from the fact that I tried doing a double overwrite (ONLY applying to Custom_Civilizations and NO OTHER FOLDER):
1. Installing the modpack, which overwrites some of the SVN modular civs, including Israel.
2. Copy-DELETE-paste-overwriting the same civs from SVN folder, 100% UNDOING EVERYTHING that Step 1 did to the OLD civs files.
Which means that from the point of view of the OLD civs (and the map in question only uses them, obviously), NOTHING HAPPENED.
Like, literally nothing - the OLD civs files weren't CHANGED at all (the double overwrite restores them to their pre-modpack state 100%).
The ONLY difference is that now there are more civs folders in the Custom_Civilizations folder, and those are added to appear in the game itself (but NOT the map).
Which should NOT affect the MAP whatsoever, since I see zero reason for it to even READ the newer civs files to begin with, cause those AREN'T used by the map.
(This is what I meant by the Pedia - civs getting loaded into the GAME, but not used by the MAP whatsoever. I obviously can't see colors in the actual Pedia.)
This is utterly confusing, but the reason why I don't want to simply just drop it, is that it might be some weird programming issue all along, so I want to rectify THAT.
But, ugh, this is hideously disturbing, indeed.