Well, an update to the issue. It's still not fixed, but after cooling off and thinking about this for a while I decided to do some more troubleshooting. I trashed all my prefs, plug-ins (after renaming and moving the folder), emptied the trash, restarted, and let it install the core plug-ins. The problem is still the same. But there is additional info I've uncovered. If I open any of these items in the setup menu: Hardware, Playback Engine, I/O, it 'resets' something and the software works as expected, i.e. listen to audio on the track to be overdubbed on until the punch in, and then see the waveform being recorded, but not hearing it through the machine, and only the input on the front end. Also if I change the record modes at the top of the Options menu (toggle Destructive Record on/off) it works. Again this works only until another track is armed or the current ones record enable is toggled off then back on.
I then did a 'full' uninstall of Pro Tools by trashing the folders described here:
How to manually uninstall Pro Tools 11 (or higher) on Mac OS X, copying my Plug-ins folder to a different location and renaming it, did a full Trash preferences operation using PTPrefs (the newest one), dumping the trash can, rebooting and then re-installed PT 2020.9.1.
The problem still exists.
It may have something to do with the driver for the Apollo? It seems to 'fix' the issue whenever the driver is referenced from within Pro Tools. To test that I think I would need another interface (I currently don't have one) and/or uninstall the UAD driver (it's the most current one).
I'm just spitballing here and hopefully someone with some knowledge can chime in with a sanity check and a confirmation I'm doing this correctly or not...
In the meantime, I'm heading off to the UAD forums and see if I can get any info there...