Have to say, not so much with this years madden. Due to previous years I was keeping the selected player on FS, because it was the safest route to go to prevent any possible anomalies like you mentioned.
After seeing Cyprien seem to act "realistic" in different coverages and blitzes I began to experiment with having different players selected. All plays well. EA doesn't seem to have any special coding for a selected player compared to unselected, other than "if user input equals true then await next user input."
I can have Poszluzney selected a whole game or not, his performance will depend upon the situation and opposition he faces.