Not true in this instance, ct-ng setups the default sysroot/include dirs properly without needing any hoop-jumping.
(You *DO* need to update include dirs for non-sysroot stuff, obviously, but that's not (yet) the issue here
).
I have no idea what's going wonky in your setup, but something is obviously off *somewhere*.
I'd try again from scratch in a Debian VM.
(EDIT: Oh, wait, see next answer: what you're doing wrong is obvious: don't pass --sysroot ;p).