Bee, some things that might be overlooked about Rookie league rosters:
They are filled with Latin players, some of whom have signed for very significant bonuses. They are hungry and can play. Might be raw but they can play.
Rosters also contain a fair number of JC players who were signed as draft and follows the prior year or who have just signed instead of transferring to a DI program.
Fillers: can play...a lot and some become prospects. Players who are "fillers" often were stars on their college teams.
If you were to compare the #6-9 hitters and the 5th-12th pitcher on a staff in rookie ball with those at a top DI, you will likely find the #6-9 and the pitchers were stars at the collegiate level, JC level or just signed a huge bonus out of a Latin country. Even at the schools you have listed, the #6-9 players/5th-12th pitchers are very good college players, but may not even be "fillers."
Professional baseball is taking the very best from a pool that is scouted nationally and beyond. By and large, even the top DI's are limited in recruiting by budget and 11.7 so they look regionally for the most part.