It doesn't really sound as though his snares are on when they're not. If you listen to the recordings there's a distinct difference.
On pre-Aenima recordings and 10,000 Days his snare drum sounds very different snares on/off, but I think on Lateralus and especially Aenima, they sound quite similar.
Yes, there certainly is a difference, and perhaps as you listen more and more it becomes easier to tell, but I've never heard a snare drum that sounds that similar with the snares on and off, and perhaps it has something to do with the recording but still, it's closer than anything I've ever heard. It leads me to believe he really cranks those heads. I agree with you though, that it is a great effect when he does flip 'em on for a section, almost like slapping your car into 5th and flooring it on a straightaway.