MinusHD, I`ve never tried waterproofing a kilt, but I think I can recommend Nikwax products, I have used them extensively in the past on all kinds of outdoor gear, any type of synthetic clothing, boots, etc. I see that they make a product specifically for cotton and polycotton fabrics, as well as about anything else you can think of. No waterproofing treatment is permanent, but I would say that their stuff is a bit more durable than the spray on products. www.nikwax.com
Here in the Northwest we have a saying regarding cotton clothing in the mountains: "Cotton kills." It gets wet, it doesn`t dry out, if you`ve nothing to change into hypothermia will come calling. Just my opinion, but cotton would be my last choice for a hiking garment. I think PV would work much better.