I think what is confusing about the minor league portion of the rule 5 draft is that it does seem to operate differently than the major league portion. In the major league portion, if you take a player, they don't have to just stay on the 40-man of the new club, they have to stay on the 25-man of the new club or get offered back. The corresponding analogy in the AAA portion would be if you take a player AA or lower, they should have to stay on the AAA active (25-man) roster the whole season, not just the reserve roster (which, I believe, can hold 38 names). Similarly, in the AA portion, you would think they had to stay on the AA active (25-man) roster, not just the reserve (37 man). If you can take a player in the minor league phase and just stick them on the reserve roster, it does operate differently than the major league phase.