Referring to this teardown (
http://torapo.com/headphone/overhead/audiotechnica-ath-l3000.htm) of the L3000, it's highly doubtful that the leather on the exterior of its wooden cups play any part in the tuning of the headphones. Observe how the rear of the driver capsule is sealed and how the baffle is significantly damped with material. Also considering Audio-Technica's MO of releasing limited edition gear with various luxury accents and finishes, it's entirely possible the leather is simply for show.
The leather earpads that serve to couple the drivers to your ears however definitely is part of the system that determines the headphones' acoustic properties.
If you have a wood headphone, try pressing your hands against the ear cups lightly during heavy bass passage and try to stop the extra vibration.
The sound does change, right?
It's the same principle here.
The leather material may not be exposed directly as a reflective surface, but it still has a dampening effect on the ear cups, and that applies even more so at lower frequencies, where the entire enclosure would start vibrating from the excess energy.
It's not just that whatever is exposed is the only thing that should be considered. Otherwise, there really is no point to that wood material inside the leather cover because the drivers are housed inside a smaller plastic blob that has a felt cover at the very back. They could simply have used plastic instead, right?
As for the ear pads, better connection between your ears and its surrounding (skin, skull) with the diaphragms means better transfer of vibration from the diaphragms... which means... more bass. That's why a good seal is so critical to having good bass, and leather just happens to stick to skin quite well...