Cannot get Mesh Bed Compensation to work correctly
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It's possible that you have gantry twist which would explain the different trigger heights. In theory you could write a bed.g which adjusts the trigger height depending on location but that sounds weird.
To find out whether you have gantry twist it probably is best if you used a dial gauge to measure rather than feel the distance from gantry to bed. Since your gantry and rod fittings are 3d printed they allow for a bit of compliance. Adding some bushing slop and possible ovality of your rods can easily make for half of your measured differences, and a slight twist which I don't think would be visible to the naked eye or feel will not show up by moving the gantry since the compliance of the printed part will allow the mechanism to slide without interference.
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no idea why this was addressed to DIY-O-Sphere, it was supposed to go to OP of course.