Yes, under 50 probably can be done
Look at it this way (Haven't played the level for a while, so I hop it's accurate)
START
Arrive at the first boss at 3 seconds
Defeat the first boss before 10 seconds
Arrive at the second boss at 18-19
Defeat the second boss at 25-26
Arrive at the third boss at 35
wait for 5 second intro (coming down and laughing)
You're now at 40 seconds
wait 3 seconds (hopefuly) for him to stop spinning
43 seconds
Heh, I'm sure zac knows this, but either way, I'm not revealing it. You get one nice jump, and with some luck (unless there is a way to trigger Eggman to do the move I want him to do) you can defeat eggman before 50 seconds (you need to be verry verry lucky, this is only theoretical, and will probably not be achieved for a loooooooooooooong time)
as for moon zone, 15 might be possible... maybe eve :o 10, but I'm not, because it may not be physically possible to get all these hits in before he holds his hands up in defense :/