As that article points out, all the Southern states that started flying that Confederate flag for the first time in the 50s and 60s in response to the civil rights movement claimed to be commemorating the civil war too. So it'd be hard for Apple to come up with a rule that excluded racists who were using it as an anti-civil-rights symbol but not actual civil war stuff, and they tend to err on the side of banning everything.
The US civil war was only in 1865. I think if the southern states had tried flying the flag any earlier than WWI, they'd have been met with opposition from people rightfully thinking they were trying to restart the war.
