Crouton doesn't necessarily go away on reboot. You just have to consistently boot into Developer Mode to keep it (and the rest of your data). You just get a war

Crouton doesn't necessarily go away on reboot. You just have to consistently boot into Developer Mode to keep it (and the rest of your data). You just get a warning and the option to do so each time it boots. That's how I've been doing it, though I hardly ever shut the thing down.