In fact, I got bored enough to test it out ..

1st half stats

1st half lineup

Substitution effected 58' (GK in for DC)

End game stats

Lineup from 58' on, with a GK playing DC
Doesn't look to me as if there's any possession penalty for out of position.
I played 2 seasons with an MC at AMC and he led my league in goals and rating.