I use Maxell CD-R Pros with pale blue bases, as well as Sony CD-Rs with beige bases and my PC Engine Duo-R reads them no problem. Even my super unreliable TurboGrafx CD will read those discs and not complain. Besides, I like to mess around with code. Why would I modify MAME otherwise(aside from fixing accuracy problems, mainly in the sound department)?
But I am seriously considering a flash cartridge, especially for SuperGrafx games, as getting the originals(well, 1941 Counter Attack, at least) will cost as much as a single flash cartridge. I will, however, still get original Gradius and Salamander HuCards.