No, as I understand it, that was the "old way" of doing it. The "new way" (which I think is called Project Crostini) is much smoother.

I got a Pixelbook a couple months ago and it was as simple as going into the Chrome OS settings, clicking the button to enable Linux support, and then it sets you up with a terminal to Linux. I've had no issue accessing the Linux environment / apps between boots.

No. You don't. It's fully secure and the host OS is aware of it as a feature. You can see your Linux files in the Files app etc..

And yes it does stay enabled.