No, there was a bug in Mach3 that would cause it to violate the acceleration limit on an axis under certain circumstances, which could cause position loss if one axis had lower acceleration than the others. I was the one who found and reported it about two years and a half ago. Brian has said it has since been fixed, but I'm not sure if anyone has verified that. I certainly have not, since I no longer use Mach3. But, certainly there is little or nothing to be gained by having either X or Y having higher acceleration than the other, since there will be few opportunities to take advantage of the higher acceleration on that one axis, even without the bug.
Regards,
Ray L.