You can edit RTP assets freely. And yes, every assets that's included with the engine by default counts as RTP. Including the generator parts, so creating characters with the character generator counts as RTP assets.
Using plugins like MV3D to make a 3D game is also fine.
Basically, your game needs to be made primarily out of graphical RTP assets (and edited RTP assets count as RTP), with custom assets being allowed, but they should be mostly supplementary. It's not strict at all, it's more about the game having an "RTP vibe" that's readily apparent. We give people the benefit of the doubt regarding this.