I have had it happen both ways, be there lose, be there win, and same for not. So... It's not really one way or the other for me, on my main Team. one of my alts does seem to do better when Im not there, but I always feel its because I over manage.
But it does seem to punish you if you make the wrong sub.

If you feel your team does better without you being there, set up your subs and check the score later.