No, the screw heads are completely below the surface. But this should
be a function of where you set the stop on the drill, not the jig
itself. The Kreg jig just sets the angle of drilling. They have some
guidelines and measurements that are recommended but you can adjust
them as you see fit. Really you are just using a stepped drill to make
a slanted hole, whose position and depth are controlled by the drill
stop and various spacer blocks. I used my jig for some 5/8" thick
particle board and made my own spacer block out of 1/4" MDF to get it
just right.

Bob