If you have them, can you share your install logs (look in %TEMP% for files starting with "Python"). If not, please share your install options.

By default, this works fine. You have to make some specific modifications to the install options to do what you've done, such as choosing to install for all users and then overriding the install path to a per-user location. If you're installing just for yourself, the installer shouldn't even have the permissions required to modify system-wide environment variables.

It's also possible that your machine has a special configuration to do this, in which case you'll need to speak with your administrator to find out why. We can't help with that - we just use standard MSIs and let the OS choose where things go.