well.
First, microtuning is already implemented via scripting in many kontakt instruments, and scripts are something you can add to any instrument.
Beyond this, to say that "Most sequencers or hosts like Vienna Ensemble (PRO) can't do this,
because there isn't any possibility to manipulate the MIDI signal
before it gets into an instrument like Vienna (or whatever synth you
like): there is ususally only a routing involved between the MIDI
instrument and the audio output" isn't correct.
if this were true I don't think an instrument in these cases (which are not demonstrable) would even respond to pitch bend values from the key editor lanes in a sequencer. It's a fact that VI, inside VEP, does just fine here.
Then, there is logical editor (aka transform) in Cubase, where a given pitch value can be substituted for another. This basically does what a script does in a kontakt instrument. EG: Guzheng by Sonic Couture. Pitch bends are limited to 'in key', or can be handled other ways. You can, from MIDI information from your keyboard *= 'black key' pentatonic configuration*, keep the authentic intonation, which is "D major pentatonic". IE., a transform function. So, what you've said is only done in an instrument has an analogy in at least one, and probably all major sequencers.
An instrument responds to what the sequencer - or controller - gives it in terms of MIDI pitch information *usually*. I don't know of anything which would fail to do this, in fact.
I have no idea about what problems of 'non-12 ET' implementation per se there would be with VI, it isn't my field. But this above information isn't really good information.