Autoleveller

My machine seems to lose about 0.36 inches after auto leveling runs. That is, I zero out the X & Y, begin the auto leveled G-code, it measures the material and when it goes to zero, that zero has changed from my original, but only in the Y. I am levelling only a portion of my material because I am u...

Is it possible to specify exact locations to probe by modifying the AutoLevelled file, perhaps locations that are not in a grid, or does that throw off the math for leveling?

Is there any way in the software to provide an additional offset for the use of a touch plate for non-conductive materials? I'm thinking of hanging a small touch plate below the bit and connected to the probe to travel with the bit as it does it's measuring.