You're correct, MIDI is very primitive in its support of microtonality, and afaik MIDI 2.0 improves it only a little: the general solution in OG MIDI is to have it send pitch wheel messages along with the note to bend it to the correct pitch, but it's limited in precision, and prevents you from using the pitch wheel for other purposes. You can do it polyphonically, but only by assigning each note in the chord its own MIDI channel, which limits it to 16 simultaneous notes.

MIDI 2.0 doesn't directly support remapping to different EDOs or tunings or anything like that, so microtonal support is still a kind of hack, but it does at least have a dedicated pitch adjustment parameter now in the note on message, with a higher precision, which is separate to the pitch wheel message - so you can use both. Still clunky but it's better.

There's also various standards for OG MIDI like MTS (MIDI Tuning Standard) or MPE (MIDI Polyphonic Expression) but it's very rare for HW synths to support these, and even soft synths that support them are few and far between.

I guess probably the most straightforward way of doing microtonal hardware sequenced synths is by using modular synths, funnily enough - none of these digitally quantised note values there! I just read the Cirklon sequencer, for example, support the MTS standard to store alternate tuning and can then output CV to modulars based off those tunings directly.