You are correct that system does have something to do with a player being put in a position to be successful in college. But "good" linebackers rarely show up at college with the technique and skill to play major college football. They show up with tools they need to be taught how to use. Some coaches are better at teaching them how to use their tools than others. Who your coach is makes a big impact on how "good" you become.
NFL scouts are so good and so thorough, they can recognize players who are playing out of position in college. The ones worth their weight are the ones able to identify these types of players. They'll find them even if they're in a system that "masks" their skills. Playing in the wrong system in college is not the deciding factor on a players NFL career. They may even be a FA signee instead of a drafted player, but there are MANY former undrafted FAs who have great careers, and many players who get drafted that don't make the roster as a second-year player.