The program I've used most that allows interchangeable fonts doesn't seem to have a problem with glyph numbering/selecting or with spacing for the fonts I've tried out, so I'd assume that there's some standardization. I have to note that a couple of years ago when I got curious about it I wasn't able to find any published standard, or even good glyph descriptions.

A couple of the relatively cheap notation programs do come with 3 or 4 choices of "alternate fonts" - mostly rather ugly; but you might assume that they'd be all to common character forms.

John