I thought of changing the tuning of a brass quartet arrangement I wrote, because I needed the sound track for further audio mixing. Only discussion I found was as old as MuseScore 0.x.
So I grabbed a simple plugin, the note colouring plugin, and added a pitch altering thing there. I simply decided to alter the C major scale tones according to a "standard" just intonation to see how it would sound. In the attached score you can hear the result. The black notes are unaltered, the coloured ones are tuned (thanks to the original plugin). The triads sound good, except for ii, which holds the bad 5th.
In the plugin I also altered the black key notes, simply by averaging the cents of the diatonic notes on both sides. There are of course theories of how to alter them properly, like C# being higher than Db.
I won't share the plugin, because I haven't checked the license of the original plugin yet. And of course my plugin needs a lot of improvement. But as long as it only alters 12 different notes (C# and Db being the same), it really is a very simple task. Any baroque temperament can easily be included. Doing this by altering individual notes through a plugin is much more convenient than trying to alter the underlying synth or soundfont or whatever. You could mark some sections, adjust all notes in that section according to a new tonic to achieve pure intervals and triads for a brass section. Creating some logic, that would go through the whole score, adjusting everything to only pure just intervals, would be nice, but impossible.
Credits to Werner Schweer, Nicolas Froment, Joachim Schmitz and Jörn Eichler for the note colouring plugin.