Let's start with the arms.
The geometry of the movement centered on each shoulder imposes that the arms rotation can intersect the circle drawn by Leonardo only in one point, whilst it is tangent to a regular circumference plotted by the navel – the true wraparound circumference, yellow in the scheme – only outside of that square, at about 65°. In addition to some minor asymmetries between right and left, both si­des of the figure show a grotesque alteration to the length of the up­per fore­arms, in order to reach the circle; and this without yet taking into ac­count the rotation of the shoulders inward by raising the arms, which in turn reduces their extension.
Should we believe that Le­on­ar­do did not realize it, or rather that he did it on purpose because of the need to satisfy the circle he designed?

Moreover, I began to wonder why the arms' extent should be re­stra­ined inside the square height;

do you do that when you raise your arms? or rather won't you manifest your 'height'?
what should prevents man from raising his arms to the sky?
there is nothing to validate this choice, which instead reveals
to have been adopted as a
constraint to resolve that
‘magic’ design, if not a
hidden worldly symbolism.

Vitruvius could not have recommended such a solution.