They're separate fandoms for the purposes of requesting, as in you can request The Flash and Arrow as separate fandoms of four.

But they're related fandoms, in that if you have Oliver as your character going into the bar, you can't have The Flash as one of your four fandoms. (Or any other DC fandom, for that matter.)

Related fandoms still can't be used to crossover with your main character, but this post is more delineating how franchises are separated out into what fandoms you can request in and of themselves.