Is this the intended behaviour?
Yes, because TA_SYSTEM is always the preferred (and best) way to save the activation data. Why? Because the activation data is per-machine already. So another user on the same machine can use the same product key to activate the app and it will still use that single activation.
If you want to do per-user licensing then use TurboFloat. That's what it's designed for.
I would like a way of undoing this mostly for testing purposes, but also because it is usually polite for an uninstaller to undo everything that the installer did, which seems not to be the case here.
Calling Deactivate(1), and making sure it succeeds, will set the files to be 0-bytes. Therefore virtually no hard drive space will be taken up by the files.