How about an extra form, which is very similar to Song Comments, but maybe called Song Tool Settings.
It would be accessed through the Song Settings areas, could save any Tools which you want to be Enabled when the song is loaded (you might want different for live versions compared to composition versions) and any Tool setting or data could go under them.
Whether in plain text or xml I’m sure it could be made to work either way. xml and embedded into main Song Data seems it may be a good way to go 