the version of Tk in /System is not relevant, as I wrote the Tkinter in the Python.org installer uses a copy of Tcl/Tk that's installed by the Python.org installer (somewhere in /Library/Frameworks/Python.framework).

This can be checked using the otool(1) command:

$ otool -vL /Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/lib-dynload/_tkinter.cpython-38-darwin.so 
/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/lib-dynload/_tkinter.cpython-38-darwin.so:
	/Library/Frameworks/Python.framework/Versions/3.8/lib/libtcl8.6.dylib (compatibility version 8.6.0, current version 8.6.8)
	/Library/Frameworks/Python.framework/Versions/3.8/lib/libtk8.6.dylib (compatibility version 8.6.0, current version 8.6.8)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1197.1.1)


As you can see _tkinter is linked with Tcl/Tk 8.6 inside the Python framework. 

I'm also using the Python.org installer (although the system I tested on has a slightly out of date copy of Python 3.8) and don't get this warning. That might be because I've been testing something different from what you're doing. 

Could you attach a script that demonstrates the problem?