Thank you for your help guys, I could successfully notarize my application's bundle with Python3 integrated.
One of the issues was, that I had to copy the entire Python.framework folder, instead of just the 3.9 folder located into "Versions". The second issue was that my copy process of the python Framework folder broke the code signing of some files, I guess because it did not copy the files' attributes, but I'm not 100% sure.
So it's important to note that what I wrote in my first post is wrong about python package from the official website. I can now say the official python website provides universal python packages correctly signed.
Best
Topic:
App & System Services
SubTopic:
General
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