Starting G-code for auto Z probe offset
The inductive sensors trigger to the metal plate under the glass bed. This implies that if you remove the slate of glass, the distance between the trigger point and the print bed is increased by the thickness of the glass slate. But, the trigger point is still exactly the same as if there were a slate of glass (as it triggers on the metal bed underneath). This extra distance need to be compensated for.

The method you are using is incorrect in determining the distance between the nozzle and bed with respect to the sensor trigger point. This answer on question: "Z Offset on autoleveling sensor setup" describes how you need to determine the distance between nozzle and bed from the trigger point. It includes a manual step to lower the nozzle a paper thickness above the build plate.

If you insist on using G-code (e.g. in your start G-code script), you can redefine the Z=0 level by adding a G-code G92. In case of a 3&nbsp;mm glass plate, you should add after the homing (G28) and probing of the bed (G29) the following:

G1 Z0  ; This will move the nozzle to Z=0 as if there was a slate of glass, 
         but in fact it is still 3 mm offset
G92 Z3 ; This redefines the old Z=0 (with glass) to be Z=3 mm