Missed page change!
On the ferrules ...
Normally just proud. The traditional versions have a small lip on them to keep them on top of the body. I'm sure you could get some flush-fitting ferrules, but you'd have to be very careful drilling your insert holes. Too shallow and the ferrule ends poke out (and would be very difficult to remove), too deep and the string tension would pull them into the body (unless you also glued them in place with epoxy).