That's all self-censoring. The law says use of such symbols is fine if it serves art², however the agency tasked with judging the youth impact of games does not think games are art. However, that's just their opinion and does not reflect actual legality, since this was never challenged in court.
So, until they change their opinion, or a game company decides it's worth it and takes them to court, game companies just end up censoring themselves in advance so they don't have to deal with it in the first place.
I find the flying of the confederate flag in real life reprehensible, but censoring a civil war game using it as a symbol of the confederate armed forces? I'm not sure that makes sense.
They don't have half their country driving around with swastikas painted on their pickup trucks, so they would certainly seem to be doing better than we are...
Your comment implies that half the people in the US fly that flag and that everyone who flies the flag is a racist and that the fact that so many people fly it hasn't made it lose much of its meaning.
Your comment makes a lot of assumptions and appears to me to be painting half the country (probably the south) as racists. This is a bigoted narrow minded attitude.
Even Kanye West has a line of clothing with the confederate flag, do you think he's part of the KKK?
So, until they change their opinion, or a game company decides it's worth it and takes them to court, game companies just end up censoring themselves in advance so they don't have to deal with it in the first place.
² As mentioned here https://news.ycombinator.com/item?id=9777854 , it was for example fine in the movie Iron Sky.