Tried this out last night. Seems to increase performance for some CD games from what I could tell. Cotton and Bonk III runs pretty nice now. I couldn't see much difference in Beyond Shadowgate, but that game doesn't have a lot going on.
I'm still getting a weird issue with enabling the 6-button pad. Whenever I turn it on, (in multiple games) it keeps pressing the right direction automatically. I can't get it to stop. In 2-button mode it's fine, it's just when I enable 6-button that the controller initialization seems to be bugged.