The last time I checked, Python was pretty easy to build. You should be able to build it yourself and properly configure it to contain only the components that you need. The most difficult part will be the SSL. See if there is an option to use Apple's built-in SSL. If not, omit it if you can. Otherwise, 3rd party crypto can bring some technological and legal problems.
You will need to roll your own Python framework from that. That, too, isn't very difficult. Just review how other frameworks are constructed. As eskimo points out, you can even use Apple's Python framework as an example. Just be careful because you aren't Apple. Sometimes Apple takes liberties that 3rd party developers don't have. For example, Apple uses a "3.8" version. In theory, that should be fine. But I don't like to deviate from defaults that are known to work unless I have a really good reason. So use "A" instead. But otherwise, that structure is good. Build the framework by hand. Copy your Python dylib to the top-level "Python" or "Python3" file. Copy your python installation bin, lib, and share folders as Apple has done. You'll need to hack up the include folder similar to how Apple has done. Don't forget the Info.plist file and the Resources folder that both need to be hacked together.
Then, you can include your real Python framework in your app and that should resolve all of the code signing problems. Currently, what you have in the Frameworks folder isn't a real framework, so that is why it's choking on it.
Ideally, you would have a true Xcode project that builds Python and then include that in your app's workspace. That would likely be too difficult at first go. Xcode will accept a 3rd party framework rudely shoved into the project. Since you are only building for macOS, you don't have to worry about multiplatform complications. Considering the fact that Apple already does all this, it is definitely possible.
While the Python people definitely know Python, they seem to know little about macOS. Bundling Python into your app the way you are attempting is definitely the correct way to do this. You just need to build a proper framework and you're good to go. These forums are full of people who've tried to use PyInstaller and got hopelessly stuck trying to get notarization to work.