I’m not a regular Repetier-Host user. I’ve played with it a bit, but I don’t like to have my laptop in the shop, and I don’t like to trust wireless solutions, so I just use an SD card for all my cutting. I do know, both from personal experience and from the forum, that Repetier-Host and Marlin can be out of sync with respect to their coordinate system. Repetier-Host does not query Marlin about coordinates. There is a special command (@isathome) that, when used, will set Repetier-Host internal position to (0,0,0).
But the fact that Repeteir-Host and Marlin are out of sync should not matter with respect to the job you are doing. All that matters is that Marlin is displaying the correct coordinates before you execute the g-code file.
As for @isathome, you could use it in the touch plate routine to bring Marlin and Repetier-Host into sync:
G28 Z ; Homes the Z axis
G92 Z0.5 ; Compensate for the thickness of the touch plate
G0 Z5 F480 ; Rases the router so the plate can be removed
M0 Remove the touch plate ; Pause to remove the touch plate
G0 Z0 F300 ; Move to Z = 0
You will have to press the knob on the display after removing the plate. Note that @isathome sets X and Y as well.