Tbh Bowser making any of the world's outside of his boss stuff is kinda sus. Like first of all he plans to "convert the residents" which if he made the world's why not just make them evil in the first place? Why go through all the trouble of converting them when you could have just made them in the first place? Plus the other world's seem to have histories of their own, good inhabitants (many of which move between paintings) and appearing in the real world in later games (as Bob-omb Battlefield and Whomp's Fortress have).
Also this:
If Bowser made the world's how would the bob-omb know anything other then the world he was born in, a world where King Bob-omb had the power star.
Honestly I just think he made the boss worlds like Bowser in the Fire Sea and Bowser in the Sky.