Here's an old sewing (not necessarily kiltmaking) tip for hems that bleed through. Try using a thin, opaque interfacing/interlining inside the hem fold. It might not work with kilts because it adds another layer when there's already so much fabric with the pleats, but maybe it's worth a try.

Of course, Barb's caution:
check what the hem edge will look like _before_ you lay out the kilt
is the best advice!