In tailoring hand sewn means that the sewing machine was guided by hand rather than a jig or computer.

I suspect that in kilt making the term has to mean without using a machine.

When sewing using a needle the layers of fabric can be manipulated so as to match up the pattern when edges of slightly different lengths are being joined, or if there is a slight variation in the weave of the cloth - I have found some pieces of cloth where the weft is not exactly straight across the warp, but in most cases the fault could be hidden by hand sewing.

On a sewing machine it is difficult - though not impossible, to ease in (shorten) one piece of material to fit a shorter one, but when hand sewing the trick is far easier to do. It is also possible to see both sides of the seam as you sew which makes the accidental sewing in of a fold far less likely.

Making shaped pleats is one of the more awkward exercises in sewing - certainly if perfection is required, though hand sewing is not a guarentee that it will be done well.