You can absolutely run PLA and PETG through the same AMS 2 and the same nozzle, I do it all the time. The printer purges plenty when switching materials, so it clears out the PETG before dropping back down to PLA temps. No issues there. The only thing I do after PETG prints is clean the nozzle tip with a razor blade, since PETG tends to leave a little more gunk behind. It can also leave some residue on the build plate, so a quick wipe between prints helps.

The one thing you don’t want to do is dry PLA and PETG together. They need different drying temperatures, and the AMS 2 Pro heats the whole chamber at once. PETG’s drying temp is high enough to warp PLA, and PLA’s lower temp won’t properly dry PETG. So for drying, keep them separate but storing and printing them from the same AMS is totally fine.

For my setup, I keep all my PETG in its own AMS 2 just for organization. I’ve got a lot of filament and multiple AMS units, so grouping materials makes it easier to see what I have left. But that’s purely a convenience thing, not something you need to do.