If your machine is misconfigured/misbuilt to be trapezoidal, that is uncorrectable with pull-offs alone. Pull-offs don’t shorten any side, and a trapezoid’s angles can’t change without side length changing (keeping the parallel sides parallel.)
This machine is a parallelogram in the ideal non-corrected case, but belt tension and build errors can lead to sides being different lengths. Since the X gantry won’t change size (…hopefully?) this means there’s no physical possibility of perfect squareness.
I actually worked through a lot of the process of squaring in another thread here — I am pretty confident in these concepts (though need to double check the implementation of the math.)
I’m not sure how to interpret your comments: if the tool isn’t useful for you, I don’t mind! I would sort of prefer if the discussion here was a little more focused on the tool and any issues using it, if you want to discuss squaring in the abstract maybe a different thread will do?