I assume you're referring to something like the New York-Penn League when you say that the Twins don't have an affiliation? I think that that's considered "Rookie Advanced." That is, it's below the level of Elizabethton, which is Class A Short Season. If you're going to argue about the Twins not being aggressive enough because they put their college picks at Elizabethton by saying that instead they "should start in the short-season A league," then I think you're off base, both about where they put their prospects and what level that league is at. I also think it's an overgeneralization to claim that each player moves in lockstep. That's just demonstrably false.