The manual config is easy: Organs just feature one pedal and 1 - 3 (or 4,5 less likely) manuals. Same for enclosures.
ODF and settings are district for reason:
ODF is a stable file format, which theoretically could be implemented by any program.
The settings are a dump of the GO internal state and may change in any way, as the GO internals change.
So storing the audio distribution rules in a separate file (or in $HOME/GrandOrgueConfig in the [OrganXXX] section) would be the simplest solution.