It might be a lot of work but you place your alignment keys on the glass
substrate using a photoresist lift-off process whereby you sputter or evaporate
a metal down first. Aluminum,gold,Ti something that will give you an opaque
target. Then when you do your first glass etch you will need to cover the
alignment marks with photoresist mask to prevent etching and distortion around
your targets. An extra couple of steps but I think it would work. Bob Henderson