So I can buy Japanese Rising Sun flag that was used under to kill more than tens of millions of Asians (and thousands of Australian), but I can not buy flag that represent an army branch in the American civil war?

The difference is the Rising Sun is a current, OFFICIAL flag, whereas the Confederate flag is the loser's defunct flag hijacked by white supremicists.

With your professed background/interests I would have expected you to know about the Rising Sun, at least.