I devised a more convenient workaround to have persistent audio tracks/channels for multi instrument output transforms. I set up bus channels for each of the instrument outputs. I do all the plugins, sends, automation, etc only on the bus tracks. When the instrument channels get transformed to audio they (luckily!) are automatically routed to the corresponding bus channel for each instrument output. So I don't do any plugin or automation to the raw (midi) instrument track. I then transform it to multiple audio tracks at unity gain, to produce "raw" audio tracks. Each of the raw audio tracks are sent to a corresponding bus channel that serves as the final audio channel for each instrument output.
For example, with an Impact XT drum kit, I have 6 instrument outputs that go to 6 audio tracks that then go to 6 bus channels. All the bus tracks go to a final Drum Bus (as usual). This is a lot of tracks, but it's easy to manage. I can make a midi edit, quickly transform the multiple outputs to their own channels, and have all the plugins, sends, and automation remain in place on the bus tracks.
I would prefer to have the transformed audio tracks be persistent so the extra bus channels aren't needed, but this will have to do for now.