A little late to the party but here's my two cents. I think sometimes it's a matter of the general talent. Many of these schools are still close enough to 11 man schools that a lot of the talent would rather transfer there and play than play six man. This happened in St. Jo's case.
Sometimes you just don't have good six man players. An 11 man QB can be all state at that level but then be a sitting duck in 6 man. Same thing goes for that runningback that might've been good with a ton of blockers but now with 3 blockers and a 5-8 quarterback lead blocking he's all of a sudden up a certain brown creek without a paddle.
It's just a crap shoot sometimes. Throckmorton is kind of isolated so i've always attributed their success to "what the hell else do those boys do besides play football". They were also blessed with already being pretty talented and having an outstanding coach.
I highly doubt if a team like Chico drops down they'll be able to beat anyone.