The python3.9.exe file in the WindowsApps folder looks like a real executable and not a link. The script also backs that

python3 read_appexec.py "c:\Program Files\WindowsApps\PythonSoftwareFoundation.Python.3.9_3.9.2288.0_x64__qbz5n2kfra8p0\python3.9.exe"
Traceback (most recent call last):
  File "s:\Downloads\read_appexec.py", line 74, in <module>
    link = read_appexec_link(sys.argv[1])
  File "s:\Downloads\read_appexec.py", line 66, in read_appexec_link
    raise ctypes.WinError(ctypes.get_last_error())
OSError: [WinError 4390] The file or directory is not a reparse point.

Although I did this as Administrator so I can successfully list the directory I am not able to run that executable. It fails with "Access is denied.". Others are working fine.

idle3.9.exe - works
pip3.9.exe - works
python.exe - Access is denied.
python3.9.exe - Access is denied.
pythonw.exe - Access is denied.
pythonw3.9.exe - works

I opened both pythonw* files in the old "Dependency Walker" and it loaded them both fine and the dependencies appear to be identical by just taking a short look beside it not showing anything suspicious in them. The non-suffix version didn't run with "Failure starting the process. Access is denied (5).".