If you ever want to run a Maya without its userSetup.py and without having to move or rename files, it turns out you can suppress userSetups by setting an environment variable called MAYA_SKIP_USERSETUP_PY to any value that evaluates as True. This is handy for testing and isolating path management problems - if you've got a rogue path and you're not sure where it's coming from, this is an easy way to make sure it's not being added in by the userSetup.
PS: If you're using a MayaPyManager to run mayapy instances, you can set this variable like so:
from mayaPyManager import MayaPyManager
import os
env = os.environ.copy()
env['MAYA_SKIP_USERSETUP_PY'] = '1'
mgr = MayaPyManager('path/to/mayapy.exe', env, 'path/to/maya/scripts')
# this manager will use only the user provided path
# and won't run the userSetup.py on startup
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