(I meant it's specific to Ubuntu).

Thin clients boot from a server chroot.
Then, when the user logs in, they connect to the server, and all the session is 
on the server.
So they use the server root, because all the user processes run on the server. 
If you don't want them to use the server root, then they're fat clients.

If you want them to boot from another chroot and not use the server
root, then that other chroot should also be a fat chroot. It should have
a desktop environment installed. You can't boot a thin client from a
thin chroot and not use the server root. Then it isn't a thin client,
and it should have plenty of ram to load a normal environment, and that
chroot should have a desktop environment (i.e. be a fat chroot) etc.

Or did I misunderstand what you're trying to do?

** Changed in: ltsp (Ubuntu)
       Status: New => Incomplete

-- 
LTSP_FATCLIENT=False sends thin-clients into root directory
https://bugs.launchpad.net/bugs/615216
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