I always like to look at the reasons why we do things. The only reason why it is traditional for the twill lines to run in a certain direction in a kilt is because that's the "good face" of the cloth -- the side that doesn't have knots and things on it. So that's the face that you'd want on the outside of your clothing.

In other words, there is nothing magical about the twill lines running in one direction or the other. The point is to have the good face of the cloth on the outside of your garment.

So when you are dealing with cloth like Lochcarron's Strome weight, where the twill line runs the opposite direction as normal, what do you do?

Speaking for myself, I make the kilt with the good face of the fabric out. That's the whole point, really. (Though, I must say, with Lochcarron's fabric one can hardly tell the good face from the bad face).