Absolutely different pads alter the sound slightly. I always thought my ears were too close to the drivers on the HE-6, even though they weren't actually touching the drivers most of the time, and it's nice to have the drivers moved a bit further away with both the Beyer and pleather pads.
With the Beyers: To cover the drivers I temporarily used the foam that came the Beyer pads, it's similar to that in the HD650. It adds a bit of a veil I think (I removed it in the HD650 for the same reason), and I'm going to put in some nylon from some women stockings instead. Loevhagen, I tried to use the rubber rings that came with the Hifiman pleather pads to further increase the distance of my ears to the drivers. I cut them a bit smaller so they would fit, but I gave up on it (I'll try again later..).
Regarding sound, I noticed better soundstage/imaging, and more reverb with the Beyer pads.
I didn't use the Beyer pads long though, as I was curious to try the new Hifiman pleather pads too. So I "rebuild" the pleather pads, and I have to say they are pretty nice too, a bit different sounding than velour. I had the impression of faster reverb, more tight/controlled than with the Beyer velour pads. I think I understand why Hifman has changed the stock HE-6 pads to the pleather ones.
I prefer velour though, and I'm going to put the Beyers back on when I've cut out some nylon for it.