Re: More experience as a drummer, less muffling of the kit..what does that tell us?
I can't speak about many pro drummers, but I do know that Portnoy muffles his snare and his toms.
On his snare he has a huge piece of black tape, and the batter heads of his toms are pinstripes, which have built in muffling rings. To top it off, his snare head is also either a Controlled Sound head or an Emperor X, both of which are designed to muffle. So his snare has a muffling head and a piece of tape on top of that!
I think it has to boil down to personal taste. Sure, one should get better at tuning with time, and one should have a better touch on the drums as he/she gets better, but this doesn't necessarily translate to, "I think I'll stop using muffling now." I think it's just what the drummer likes. I've been playing for some time now and I still muffle my snare with 1/2 piece of moongel. I just like the way it sounds and it has nothing to do with my tuning abilities as I never muffle my toms, they sound great with a coated ambassador, which, BTW, has a coating and therefore, will muffle some. The more stuff you do to a drum head the more you lose the high and mid ends. This is why muffled heads or very thick heads seem to sound deeper when in actuality the lower tones are just more pronounced because the mid/high have been dampened. But I digress.
In short, it's about what sound the drummer wants-period.