I’m not positive of all implications of your description here, but, in case it is of interest, here is what I found on this specific bug:
First, what I’d done originally, was make a track using the male voice, then I wanted to use the same track (including all automation and MIDI data, like pitch bends) with the female voice, so I duplicated both the (virtual) piano accompaniment track and the Omnivocal track, and used a MIDI Modifier to transpose both tracks to the female range and changed the Omnivocal singer to use the female version. (I also disabled the original piano and Omnivocal tracks.)
My expectation was that I should now hear Omnivocal in the female vocal in the female range, but I did not. It was still in the male range.
Next, I went into Omnivocal on the female track and used its transpose control to make the same transposition I’d done in MIDI modifier. I now heard it in the right range.
Then I tried turning off the MIDI Modifier, thinking maybe it wasn’t being paid attention to at all, but now the Omnivocal part was also not in the right range (If I’m remembering correctly – it could be that there was doubling in different ranges???).
So finally I turned the MIDI modifier back on and rendered the recording. I didn’t notice until later, that I was also hearing the sine tone that Omnivocal makes when you’re just playing it while recording a MIDI part mixed with the female vocal (that was not showing up in the rendered version with the male Omnivocal). I haven’t gone back to it to try any further troubleshooting as it was just meant for a quick initial test of Omnivocal, not a polished recording.
I also didn’t try anything like just manually transposing the MIDI on the instrument track I was using for Omnivocal to see if that would have done the trick without having to use a MIDI modifier and/or the transpose control within Omnivocal.
In general, I believe that simply transposing the MIDI, be it manually or with MIDI modifier, should have been sufficient (i.e. in terms of user expectations – I don’t know what is going on under the hood with Omnivocal that caused it not to behave that way).