yeah, i figure that wood cups is a worthy upgrade, it's more about whether lawton wooden cups or martin wooden cups are a better choice. although perhaps not many people have heard both, given it's a significant outlay either way. i haven't come across any direct head to head impressions from someone who has heard both.
you should have got mark to do one of yours, so we could compare!
maybe i can get one from each! aha. (don't tempt me!)
Not sure about Mark, but Martin will build the cups as deep as you want. My D2000 cups are way deeper than stock, call it about 1/2" and not only sound but look great (not that looks matter).
I doubt there is much difference in cup design inside but that's a pure guess. The belief (not sure if it's placebo or not) is the type of wood makes a difference, which is why luthiers use different woods. COCOBOLO and Bolivian Rosewood I was told are the best sounding. I am a skeptic on this.