I believe I have figured it out, although I'll see how everything acts for the next few days.
I did have to use a separate bluetooth controller for each switch pro controller. I did everything using bluetoothctl. I left scan on both bt controllers, discovery off, and agent to NoInputNoOutput. I then connected one switch pro to each bluetooth controller and trusted the switch pro controller. Seems like I can now turn off a controller and turn it back on and it will connect automatically, nothing manual required.
I can't figure out the analog sticks with two controllers. I saw a post about using xboxdrv and a udev rule and a systemd service file, I tried that, but only one controller was being recognized as a "Switch Pro Controller", the other still only recognized as a "Pro Controller" (so no analog up or right). Also, for some reason when I had all of this enabled and I would try to configure the inputs on a switch pro controller it would say that 5 gamepads were detected. Couldn't get anything to actually work in a game either, only in emulationstation. Once I uninstalled xboxdrv and deleted the udev rule and systemd service file and restarted retropie then worked correctly, only seeing 2 gamepads and they work in games.
Maybe one day the analog sticks will just werk without messin around with it. Until then I just won't be playing n64, which I guess doesn't work all that well anyway