How about uniquely rewriting just one setting, transferring it, and then checking if it's reflected?
If you replace equal temperament with something else, you should be able to immediately hear that it's been rewritten after transferring everything.
All settings that had equal temperament selected should be replaced.
It should depend on the preset number of the alternative tuning setting.
If the same alternative tuning settings are selected for the other timbres, consistency should be maintained.
However, your worries may not go away,
If you want to confirm whether transferring the factory alternative tuning settings file will revert it to its original state, it might be best to get a direct answer from the manufacturer.
However, the overall atmosphere is clearly shaped by the melody played, the playing style, the expressiveness, and even other timbres and rhythms.
I believe that expressing this using only a single timbre would result in a very exciting piece.