Actually most of the time if you're playing in a different tuning (eg quarter-comma meantone or pythagorean or whatever) where they would be different, you're p

Actually most of the time if you're playing in a different tuning (eg quarter-comma meantone or pythagorean or whatever) where they would be different, you're playing a type of music where you exclusively would play one note or the other, so the fact that they are theoretically different doesn't arise.