All, I was following "What's new", not "Forums", and I just realized I'm trespassing .... I used electrons in my bench build. Sorry (and I'll chop wood with an axe for 3 hours as penance)!
Hasin,
I would be worried about the force couple (or torque), and the resulting bending moment on the screw. The dog block will try to bend the screw, and have more leverage to do it.
Most of my usage of the tail vice (never had one until recently) has been clamping work flat on the bench top. So this moment is the offset distance from the bench surface to the center line of the screw multiplied by the clamp force. Dropping the screw down, and using a taller dog block, increases the offset - and the bending moment. I don't know when this would become critical, or even inconvenient, but I'll bet BC would be happy to answer...??
Failing any input from them, in your position I'd probably cut the dadoes/rabbets on bottom of the bench deeper, where the tail vice rails mount, so that the specified mounting position, relative to the top surface of the bench, is maintained. Hope this helps, and enjoy your build!