You might get better movement by having the two layers more separate - rather than joining at the lower edge, let the lining hang from the fell.
I usually press in the pleats before sewing, and I'd fold and press the inner folds into the lining making the separation just a fraction smaller than the outer layer, so the visible folds of the completed kilt are just a little lacking in the inner layer. That should mean that the pleats are inclined to remain on line.
I deal with pleats which kick out by lifting the inner fold at the waistline so there is a slender triangle of fabric raised up. For me that is to counter body shape, to get a two dimensional fabric to wrap around a three dimensional shape, but it would also negate changes in the structure of the fabric.

This is the under apron and its pleat, viewed from the outside of the kilt during construction.
That is probably more use for future projects, so as the kilt is finished, you might be able to sew in a couple of lines of thread for a few inches vertically down from the fell and close to the inner fold to contract its length enough to resolve the problem with that unruly pleat.
Anne the Pleater :ootd:
I presume to dictate to no man what he shall eat or drink or wherewithal he shall be clothed."
-- The Hon. Stuart Ruaidri Erskine, The Kilt & How to Wear It, 1901.
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