You have to devide between org guys and real prospects. Sometimes an org guy makes it to the majors but most of them are there so the prospects have competent teammates.
Many seniors are picked because the are good baseball players who are reasonably polished so they become competent teammates although they don't have the tools for mlb.
You can't just field a team of raw athletes because that would mean terrible baseball and a bad learning experience for the prospects. Ideally you want just good prospects but in reality in later rounds teams have to decide between athletes and players and teams will pick a good mix, some athletes who could turn into players and some steady eddies who can throw strikes and put the ball in play.
Of course those steady eddies still have good tools by college standards but not by pro ball standards. And likewise the athletes still have some baseball ability just not for pro ball (the athlete pitcher will throw 98 and probably will walk 5-6 per 9 innings and the steady eddie pitcher will throw 88-90 with solid command so of course it is not two walks per inning vs 75 mph like in HS).