Honest question:
Do you consider pairings between characters that are “part” of each other in some way to be incestuous?
As in, Roxas and Xion, Roxas and Namine, etc.
Not really. I think it's fair to consider clones - in general, not just in kh - related if they consider each other family, but that's not really the case with kh. The only exception is Vanitas calling Ven and Sora his brothers, but we know Vanitas wasn't even originally part of Ventus anymore. So it's a bit of a gray area.
Roxas and Xion are generally more "best friends" than "siblings". Though the fandom does like to make Lea, Isa, Roxas and Xion into the "seasalt family", that's not a canon thing.
And biologically speaking, I don't think they're related? Even if they used to be back when Roxas was walking around in Sora's body, they all have their own Replica bodies now.
I've always found the "which one is REALLY incest" debate between Rokushi and Rokunami shippers a bit pointless. Neither of them are incestous.