There's some debate on this, including that MAME (and pretty much every other software emulator) have always gotten it wrong. I'm hardly a high-level player, esp. at CPS1 SF, but a close friend of mine is, and he swears up and down that the Mister runs the game more or less the same as a real CPS1 DASH board with the 12mhz crystal. The non-DASH PCBs have a 10mhz crystal.
I have no idea how you can tell the difference, but there you go.
Has anyone reported this to Jotego? Were the CPS1 customs ever fully decapped?