Absolutely,otherwise you'd have to buy an awful long piece of fabric to get enough for the ruffle.The seams are hidden in the gathers,once it's all gathered up.Also when you get to the corners,clip the seam allowance on the ruffle so you can make it around the corner easier.HTH
Kathi

Yes. There are even designer (read expensive) pillows and cushions out on the market with seams in the ruffles... some stand out like a stop sign which is frustrating when you pay top dollar. So don't worry about it.

Just make sure you do some kind of seam finish on the raw edges of the seam - serge it, or turn under & stitch.