As a long time organ player, I also was surprised by the default tuning in Zynthian. On the one hand, I know that Fons had chosen it with reason.
On the other, many organ players play organs in equal temperment, but of course you’ll also find historic instruments (often restored to their original tuning). Not many organists have the luck to have access to such an instrument.
Last but not least, a temperment other than equal is useful for baroque music, but not that handy for music of later periods.
Concerning Hauptwerk, it is based on sample sets of real instruments. I’ve never used it, but I would expect that each Hauptwerk set by default is tuned to the tuning of the sampled instrument.
Aeolus, however, was not modeled after a real instrument, despite that fact its default rank set is similar to what you could find in a german baroque instrument.
My digital pipe organ console can be set to various temperments, but it does not remember the setting. Instead I have to change it after each “Reboot”. This obviously was implemented with reason, as it would confuse some players in case the instrument (e.g. in a chapel) was used by different people.
Since changing the tuning in Aeolus requires that it re-renders its precomputed “waves”, I’d vote for equal temperment being the default and either leaving it up to its native UI to change it or even providing an option in Zynthian to choose anything other than equal.
Just my two cents,