As someone who has kept a close eye on Make America Again, the reasons for the changes are this I think:
1. Kemalist Wisconsin if I remember right was the brainchild of a Turkish dev who got banned for saying stuff about Armenian genocide denial or at the very least they did a lot of dumb things that got people to dislike them to a degree they were kicked off the team. This kind of put Kemalist Wisconsin in a bad position since the person who thought of the idea wasn't on the team anymore.
2. The Fire Legion or Burning Legion (whatever its called) with Sam Brown seems to of been a reference to FNV and Joshua Graham. Some I imagine probably thought it was disrespectful to Sam Brown who was injured in Afghanistan. Changing something on the basis of it "making fun" of someone could be a slippery slope all things considered because besides the situation with the Brown, this is a mod where a real life commander of Area 51 can transform the site into Hyperborea and the Native Americans of the Southwest US get typically destroyed by the Atomwaffen, all the while you can see Osama bin Laden lead a country in Cuba and John McAfee lead "Ancapistan".