I agree with this for the exact same reasons you mentioned. In saying that, I think comic series that differ from the main continuity and are essentially canon AUs should be nominated under their corresponding titles. For example DC's Bombshells takes place in an alternate universe, so the disambiguation should reflect that. For example the character Kate Kane (DC Comics) would be the Kate from the main continuity comics (titles such as Batwoman, Detective Comics, etc.) while Kate Kane (Bombshells) would be specific to the Bombshells AU.

EDIT: Coming back to this comment now after catching up on the previous post, and my preference would be to nominate all ships under the main fandom title e.g. DC Comics, and then use the disambiguation to designate a specific title if necessary. This will also allow people to nominate based on canon era if they desire, while ensuring all the noms for that franchise fall under the same umbrella.