I know of your qualms with the game over on the Wharf Roach, but don't worry I'll make the game overs boss battle only in the future, so in the case of the Wharf Roach, it will be as you said, the scene that plays when defeated by the Wharf Roach G. There will probably be 1 or 2 more game overs after that, but only post remake.
Technically it would be doable, but even although I would like to have the incubator mechanic go that far, I don't think I'm heading that direction, at least in the start, because of the CG requirements. Without images to support the changes and potentially having to edit/arrange several variations of the scenes it would be an extreme amount of work.