To follow up, updating [config]/core/interpreter_[os].cfg to point to Shotgun’s python 3 path instead of Python 2 will ensure the app will run in python 3. For example, on windows, change C:\Program Files\Shotgun\Python\python.exe to C:\Program Files\Shotgun\Python3\python.exe in the file interpreter_Windows.cfg.
It looks like those interpreter files will be unnecessary after Nov 1st, 2022, when SG Desktop is updated to use python 3.9 by default: IMPORTANT NOTICE - Upcoming removal of Python 2.7 and 3.7 interpreter in ShotGrid Desktop