Perk plays Dwight Howard as well as anyone in the league. He always seems to get a fair number of rebounds, but I can't remember too many times watching Howard against the C's and thinking that we just couldn't stop him (whereas you watch Howard against most other teams, he often IS clearly the most dominant player on the court).
So, Van Gundy's doing his job, doing what he can to get the refs to call a tighter game. The ridiculousness of saying that Perk doesn't have to worry about foul calls is off the charts, since we haven't had a legitimate backup center all season (and still don't).