MIDI doesn’t force you to use 12TET anyway. You can use MTS. Support seems widespread, at least among the equipment and software I use, some of it dating back to the 1980s.
MTS is how you specify how MIDI notes are translated to frequencies, if you desire. You can use it to specify alternative scales, if you desire. The Wikipedia list of hardware and software which supports MTS seems very conservative IMO... my personal experience is that MTS support is reasonably common.