If you take away the box, the cylinder is exactly the same as the cylinders constructed around an arbitrary minor axis, so they're corrected in the same way. Ignore the lines of the box as best you can while you correct the minor axis, because it can and will throw you off and try to tell you that it's properly aligned.

I was talking about box 2, sorry, I misread your page. Here is where I'd approximate the minor axis to be on each plane. I'm a bit tired so it could be a bit off, but you'll notice they take slightly different angles and are offset from one another. In an ideal world, the minor axis correction would just be the same line you drew through the midpoint of the planes on each end but we're imperfect humans and will often have some level of inaccuracy.