Well, "misery loves company" I guess.
it's a catch 22... If you don't work on the rosters in terms of missing players or minor leaguers you think might get a call to the show (even though apparently SDS doesn't think so) then you won't be able to import anyone once you're in franchise. Of course, when you do all that work PLUS the 40 man, lineups, rotation, etc. it's blown to H*** and back once you go into franchise.
I think your suggestion is a very reasonable one. Get the people you want into your roster but wait on the 40 man, line-ups, etc until after you're in franchise and out of spring training.
I'm just wondering how hard would it be to have an option that says something like, "do not change saved loaded roster" when you go into franchise mode. I'mn not a coder so maybe the answer is "impossible."