lib/sysroot: Match deployment /usr mode for overlay
lib/sysroot: Match deployment /usr mode for overlay

Rather than hardcoding 0755, let's directly look at what `/usr`'s mode
is and copy it when creating the overlay.

Closes: #1843
Approved by: cgwalters

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