I don't know if you are talking about this, but pywikibot checks if user-config.py exist before it starts. If it's not present, it'll run generate-user-config.py, and not the script for which it was called.
So the problem that you describe probably does not concernant only login.py.

In T166458#3296694, @Framawiki wrote:

I don't know if you are talking about this, but pywikibot checks if user-config.py exist before it starts. If it's not present, it'll run generate-user-config.py, and not the script for which it was called.
So the problem that you describe probably does not concernant only login.py.

Yes, that's it, I haven't known this is a behavior of all scripts, but it haven't seemed logical to me in the case of login.py.

In pwb.py a comment says, after having launched generate_user_config:

1. because we have loaded pywikibot without user-config.py loaded, we need to re-start
2. the entire process. Ask the user to do so.

Is it steel true ? I can't figure out what user configuration is loaded before this snippet.

Perhaps it could be loaded right after it was created? Or perhaps the original command should be stored and run after using subprocess.run() or something similar neutral?