Assuming that the height of 1.375 dimension is with the scriber clamped on top of the arm, with the inclined face uppermost:
The scriber, presumably could be clamped below the arm, again with the incline uppermost. This ought to move the scribing point down by (Thickness of arm + thickness of scriber) to reduce the height.
Otherwise you can use a bit of gauge plate to make a scriber cranked to such a depth that when "1.000" is indicated, the cutting edge of the scriber rests on the surface table.
If you are a glutton for punishment, why not make the cranked scriber in two parts so that the blade can be screw adjusted. Then coat the screw with an anaerobic and adjust it so that the scriber contacts the surface plate at the "1.000" setting. Once cured, you merely have make an allowance for the scale reading 1.000 in what is now the Zero position.
You can have hours of frustration trying to get it right!
Howard