Soooooo I more or less merged my modmod with the current Git version. What I did was download the current state of DoC as zip archive and unpacked it as its own mod. Then I copied all files I changed (exclusively XML plus the art assets for my police unit) and let them overwrite the downloaded folder, followed by renaming it, editing the .ini and scenarios to get it to run.
Then I started the thing, skimmed trough the Civilopedia and saw that everything was as it should be, and decided to try a test game as Rome, partly to see if the accursed city of Carthage would now be where it ought to. Weeeelllllll... the good news is that Carthage really was in position (while you still have to go to the Gulag for your many crimes this does qualify you for doubled rations on Taco Tuesdays), but my starting units... I had four Jaguars and three Skirmishers instead of Legions and Archers.

How did that happen? After giving myself Archery with Worldbuilder (cool new thing btw, you shall be given double rations on Soup Saturdays as well) and looking in the city screen and around the world it seems this doesn't affect what you can build in cities, there I had the usual list of Archers, Warriors, Axes, Spears, Legions (the last three greyed out because no metal), only starting units. (AI Carthage also had a Skirmisher or two)
I then started some more games to see what starting units this or that civ would get, and the results are as follows:
Egypt - Warrior (everything in order)
Greece - Axes instead of Phalanxes
Persia - Skirmishers instead of Archers and Impis instead of Immortals
Arabs (600AD) - Skirmisher instead of Archer, but Camel Archers as ussual; playing a few turns with Arabia and giving myself Explorers around the world revealed Viking Patiyodhas, Aucacs and Legions, Tibetan Aucacs, Skirmishers and Numidian Cavalry, Korean Legions, Skirmishers and one regular Archer for some reason, China with Skirmishers, regular Spears and regular Archers, and Japan with Samurais, Cho-Ko-Nus, Skirmishers, Aucacs, and one regular Archer.
France (1700AD) - Redcoats and Conquistadors in Paris, oh my! All other cities of mine have rifle garrisons though.
Well... something somewhere obviously went wrong.

Could it be that the three new units I added messed up the numbering the game uses to assign each civ its starting units or something? I don't see any misplaced unique buildings in France for example, Notre Dame and Versailles are where they should be, in fact absolutely everything seems to be working fine, with the exception that most starting units are unique units of a different civ than the one they belong to.
So, erm, Christmas miracle?