If it isn't fair for autofilled people to face people who main their roles, then guess what, the openly have the option to disable it. What makes it fair right now if I get autofilled against someone who is autofilled, they just got an advantage because they are lucky, also giving the option to leave it in would help in lower populated servers where queue times are already long or for players that are flexible enough to play every role comfortably if it means lowering their queue times.
also In the current ladder there are still players being autofilled and some that aren't, some players are getting auto-filled more often because of the roles they chose, so should they have a different ladder???
Your missing that everyone has the option so no one would have the advantage. it like if I give everyone the option of getting 5 dollars for free, if people chose against it, they aren't at a disadvantage, they just didn't want the money.