That seems to be the road we are heading down, but I think some of it may be intentional. It's a way to shut up the masses without relinquishing control of the OS back to the user.
Google's way of going "Here, we'll just "let" you run Linux" but it's also getting people used to the idea that Linux is just an "app" you run, the underlying OS still remains locked down as ever. The dangerous parts of Google's change isn't just not being able to run your own software, it's device attestation and the power that gives them (and Governments) to control what your computer can and cannot do.
If Microsoft ever implements similar changes to Windows I'll view WSL the same way.
It's just an illusion of freedom to placate us nerds.