I twist the seams all the time, as long as the material isn't a very see-through light or white, where it would be highly visible. If it's a very thin material, then I have been known to iron the whole seam the other direction just to get them to nest.
I was worried when I first turned them but found out that when I put them on the longarm, the loft of the batting (I use Warm & Natural) and the backing seemed to just even them out. I can't even tell after they come off the long arm where I twisted them. I am a beginner using Pantographs and usually quilt a more open pattern. It you wanted a dense quilting pattern on the quilt, then I might would think twice about twisting them.