It appears that crouton doesn't actually replace the OS, so you're both right.
FWIW, I've owned one of the Samsung ARM Chromebooks since the week it was released and I've been running crouton for a couple of months now and it works really, really, well. I still use the ChromeOS side for very simple browsing (the Aura window manager is nice if all you need is the web) but switch over to the ubuntu/X11 interface often to do development work.
1) Have you noticed any effect on battery life or boot time with the chroot environment in place? 2) Can I access Ubuntu CLI programs from the shell within ChromeOS or do I need to switch to the full Ubuntu window manager environment? 3) Any other disadvantages you can think of?