When you find where your python 3 framework is located, I would edit the .bashrc file in your home directory and add:
export PYTHON_LIBRARY=<Path to your Python framework>/Versions/3.8. You may need to add Python at the end, that is the actual shared library.
or, move it into one of the standard locations.
UPDATE: I did some more digging into the PythonKit code, and the search paths that it looks for Python frameworks is the current working directory (would probably be $SRCROOT if you are running in Xcode), or /usr/local/Frameworks (probably assuming a Homebrew installation of Python). I added the the system locations (/Library/Frameworks and /System/Library/Frameworks) and everything worked fine.
The relevant line in PythonKit to modify is in file PythonLibrary.swift, and its the setting of librarySearchPaths in the Darwin section.
You might want to contact the PythonKit developers and ask them about what their intentions are about using PythonKit with Xcode and MacOS. You can install Python using Homebrew, or copy an existing Python.framework into /usr/local/Frameworks and it should work okay, too.