Ok. Well, I don't have the Xcode command line tools installed. This is what I see:

 % ls -l /usr/bin/python* lrwxr-xr-x 1 root wheel 75 Jan 1 2020 /usr/bin/python -> ../../System/Library/Frameworks/Python.framework/Versions/2.7/bin/python2.7 lrwxr-xr-x 1 root wheel 82 Jan 1 2020 /usr/bin/python-config -> ../../System/Library/Frameworks/Python.framework/Versions/2.7/bin/python2.7-config lrwxr-xr-x 1 root wheel 75 Jan 1 2020 /usr/bin/python2 -> ../../System/Library/Frameworks/Python.framework/Versions/2.7/bin/python2.7 lrwxr-xr-x 1 root wheel 75 Jan 1 2020 /usr/bin/python2.7 -> ../../System/Library/Frameworks/Python.framework/Versions/2.7/bin/python2.7 lrwxr-xr-x 1 root wheel 82 Jan 1 2020 /usr/bin/python2.7-config -> ../../System/Library/Frameworks/Python.framework/Versions/2.7/bin/python2.7-config -rwxr-xr-x 1 root wheel 137536 Jan 1 2020 /usr/bin/python3 lrwxr-xr-x 1 root wheel 76 Jan 1 2020 /usr/bin/pythonw -> ../../System/Library/Frameworks/Python.framework/Versions/2.7/bin/pythonw2.7 lrwxr-xr-x 1 root wheel 76 Jan 1 2020 /usr/bin/pythonw2.7 -> ../../System/Library/Frameworks/Python.framework/Versions/2.7/bin/pythonw2.7 % ls -l /usr/bin/pip* -rwxr-xr-x 1 root wheel 137536 Jan 1 2020 /usr/bin/pip3 

I had assumed that /usr/bin/python3 was part of the system, since it is not a symlink. But then when I do this, I see it is indeed hitting Xcode:

 % /usr/bin/python3 objc[12852]: Class AMSupportURLConnectionDelegate is implemented in both ?? (0x20ab7e7a0) and ?? (0x1143782b8). One of the two will be used. Which one is undefined. objc[12852]: Class AMSupportURLSession is implemented in both ?? (0x20ab7e7f0) and ?? (0x114378308). One of the two will be used. Which one is undefined. Python 3.8.2 (default, Oct 2 2020, 10:45:41) [Clang 12.0.0 (clang-1200.0.32.27)] on darwin Type "help", "copyright", "credits" or "license" for more information. >>> import os >>> print(os.environ['PYTHONPATH']) Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/Applications/Xcode.app/Contents/Developer/Library/Frameworks/Python3.framework/Versions/3.8/lib/python3.8/os.py", line 675, in __getitem__ raise KeyError(key) from None KeyError: 'PYTHONPATH' 

So Xcode is definitely involved.

EDIT: So I uninstalled Xcode. /usr/bin/python3 is there, but it is clearly a stub file of some sort. If you run it without Xcode or Xcode command line tools installed, you get a popup to install the command line tools. So python3 is not part of the system, but the stubs for it are. Thanks for the patience.

Even more interesting, if you have Xcode, but not the command line tools, the stub launches Python3.8 from the Xcode installation. Once you install the command line tools, it then switches to launching that version. Presumably this is all because of the read-only system volume.