Richard Durrett was able to get in a few questions for John Manuel in the aftermath of Baseball America's top 100. His answer on Main (thanks for asking that question Mr Durrett):
Q: How did Michael Main drop out of the top 100?
A: We all liked him. He's pretty athletic with a power arm. But he threw 59 innings last year and hasn't advanced past low Class A. It's a high standard. His durability was a question, so those were things that kept him out. I had him 71 on my personal list, by the way.
One of his other answers suggests that Main was right behind Beltre as a runner-up for the list. Something that I noticed in browsing their list is that there are several rankings that don't fit any of the three top 50s from Jim Callis, Will Lingo or Manuel. Someone in their room must have had some real outliers.