About Neo Bomberman, I really don't know where it is placed in the storyline, because Bagular seems to want to recover Pretty Bomber, who has somewhy joined the good guys (which is canon along the newer games).

as you pointed out, Bagular's body is disposed, with only his brain making out of the spaceship to return in Super Bomberman 4, so that first option is a no-go.

Maybe he rebuit his body? He seems smart, anyway

Then, as you also said, there's Saturn Bomberman FIGHT!, a game that I find somewhat interesting (although Miss Honey looks like fat), because one of the characters is a non-evil Golem Bomber (he is shown to like animais and to be living in a forest of sorts). With this, my best bet is that two or more of the Five Dastardly Bombers survived and continued with their lives.

Considering she is the only Dastardly Bomber that has no visible robotic parts, it is highly likely that she was built with a human body (and I prefer to think of it that way), although it can be a mere easter egg of Haruka Sawaguchi, the actress and singer that used to represent Pretty Bomber in some promotional videos, music clips and commercials.