Short answer: I would think the quickest/easiest way to do it would be to temporarily set the Project Settings > Tuning adjustment the way you want it, select and bounce down just that one section of that MIDI/Instrument track to audio [using the Bounce-in-Place command], and then reset the tuning back to normal.
Other than the Project Settings > Tuning adjustment that you're already familiar with, I guess another way to be able to do what you want would be if a particular virtual instrument includes its own scale/tuning options within the plug-in [you could isolate that MIDI passage on its own track and implement it there]. Of course I don't know what VI you're using, and I'm not sure which VIs [if any] might even offer that capability -- you'd have to do a little research if you think that would be worth investigating..
That said, it may be possible to adjust fine tuning within the MIDI spec, apparently via the use of MIDI RPN messages. I can't give you any details on it -- I've never had occasion to explore that particular aspect of MIDI -- but I found some discussion of RPN messages on the MIDI Association website [ MIDI.org ]. Digging into the MIDI spec may be more than you want to get into, and I'm not even sure if you can change the tuning of just one pitch via RPN messages, but if you're up for it, I guess a little exploration might be worth the effort.
If that interests you [maybe for future scenarios], a couple of suggestions:
- Do a Google search for "MIDI RPN fine tuning" -- it should turn up a lot of responses
- Go over to the MIIDI Association website [ midi.org ] and search "RPN fine tuning" there as well