That isn't really a sensible way to calibrate as it mixes getting the filament dimensions correct with the axis dimensions. If your box is 0.5mm too big is it because your axes move too far or because you filament is wider than it should be?
I use a single wall 20x20x10mm open box to get the filament width correct. Then I use the Mendel M4 circuit board spacer to fine tune the flow rate if necessary. It has four holes so it is good to see how they come out.
40x40 is probably a good size to put a try square against to check if the axes are parallel and you could measure the diagonals.
I tend to assume the axes move the correct amount as it only depends on the belt pitch. I think the plastic shrinks more than the inaccuracy of the belt anyway. To calibrate that I make something the full size of the bed and put in a scale factor for all objects made with the same plastic. That is very small though. For white ABS, I have 1.0057 and for HDPE 1.053.
The other thing to check for is backlash as it seems a lot of people get it and printing a square does not show it up other than it comes out smaller than it should be. Circles show it, but are confusing as to which axis it is. Printing a capital H seems to be a good way of finding it on X and printing it on its side would show backlash in Y.
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