yes. You can play notes via midi and transpose via CV, or play via CV and transpose via midi.
Both functions are essentially the same as the note numbers from midi and CV are added. You can activate this using ‘transpose’ as CV-in function.
µTune does (currently) not process chords. Quantizing to pressed midi notes is a good idea and I am putting it on the Todo list. Auto-generating chords on the other hand is imho more something for a strictly 12TET based module.