Scott,
Registrations have several options when you store them.
One of the options is 'Tune Trans'... if set to ON before saving it will remember both tuning and transpose settings.
You can re-save registrations with this parameter set to OFF.
I like this feature very very much, because each song in our songbook has it's own registration(s) and they contain style, variation, intro, voices, transpose, tempo and multipads..... all ready within 1 second.