In regard to the concerns about the 40 man rosters, it's more an ai problem than a roster set issue. I'd suggest a thread in the bug report forum explaining that the ai is not properly filling out 40 man rosters.
It's possible for us to actually set the correct 40 man rosters in the game and then use that file in the roster update. We were considering doing so but haven't got around to it since it's a pain in the butt to do. Perhaps we can take the time and actually do it at some point
No promises though.