Squareness of a machine is very easy to measure. (Basically, all you need is accurate paper with squares and a web cam.) Certainly, measuring it is much easier than getting the machine really square. For example, my machine at the moment is 0.1445% square. In other words, for every 100mm of Y movement the gantry moves 0.1445mm in X.
How about being able to tell the TinyG that?
There would be a setting for squareness, default 0. I would set it to 0.001445. TinyG would then use that, and magically, the gantry movements (and the coordinates displayed) become accurate in real world.