sysroot: Update some code to use fstatat_allow_noent API
sysroot: Update some code to use fstatat_allow_noent API

It's much easier to read and use correctly.  Making this change
since I saw an unprefixed error in an issue.

Closes: #1757
Approved by: jlebon

GNOME/ostree,GNOME/ostree,GNOME/ostree,GNOME/ostree,GNOME/ostree