I think that the appendix 1 layout is simply a typical arrangement of pleats and apron, just an example of the sort of combination to aim towards.

In the text there are the numbers of pleats and widths of aprons for various different sizes, and the 3 inch panels are simply a convenient size, which can be altered if necessary.

For the purposes of the description of making the kilt it was no doubt necessary to make some arbitary decisions about the size of the pleats, and so, once you have got your own measurements you can compare them with those suggested and then, if you wish make alterations to customise the arrangement for size and maybe shape so as to get the best effect for your efforts.