I'd be fine for splitting them across waves and not having any more waves that are a combination of comic and live action. I'd want them to continue to be made with the overall same design, articulation and such, though. I'd hate for them to end up being no longer compatible at all.
I'm primarily a comic figure collector, but there are still quite a few MCU figures that I have fudged into my collection because no comic version of the character has ever been made. There are too many examples of that to fully list but I'm thinking of characters like Mantis, Executioner, Nebula, Collector, Grandmaster, Korg, Killmonger, The Cull Obsidian (the full group not just what they called Black Dwarf), Jimmy Woo, Nadia/Hope Van Dyne, Nakia, Okoye, M'Baku, Attuma, etc, etc.... Now my preference of course would be to just have comic versions of all of those characters, but that doesn't seem to be happening. I've become generally OK with using those live action stand-ins in my comic collection mostly because the modern comics generally end up adjusting the traditional comic version of the character to look more like the MCU version now anyway.
I do tend to agree thought that comic, movie and video game figures should all be in separate waves. Honestly though, I don't know if it even matters if BAF parts aren't included.