I think that's just one of those gaming urban legends. It could be true, but I don't think anyone from capcom has ever specifically said they used x68000s.
I'd really like to find one myself though. They look like a lot of fun.
My understanding is that the power supplies fail VERY frequently. The only game I really require from it is the version of Castlevania, and that's pretty good on the PS1 disc. You can even choose the sound hardware by holding down some buttons when you select it on the menu. Which is REALLY cool.