What are you talking about? - the base plate is thick and stiff - for a reason. It would have to be over tightened to an insane amount to make the base plate flex that much. And on a "torque stop" design you couldn't torque it that much anyway. Go see how far a torque stop filter turns with a bunch of added torque after it hits the seat - hardly any more, but enough to leave a mark in the seat. Probably couldn't even do it on a flat gasket before crumbling the can shell - it would have to be way past 1 turn (way over torqued) to make the base plate flex in any meaningful way.
BTW, some filters with a P-gasket call out a torque spec, which will cause the can to bottom out and even turn a bit more after the can contacts the seat to ensure the filter stays tight.
It does scrape and leaves a mark on the mounting base when the can OD starts hitting the seat. I've seen it happen many times on engines using a P-gasket ("torque stop") design. Go install one and drive it into the seat and see for yourself that the can leaves a mark in the seat.