Many of my tops have had twisted seams. It has never created a problem for me, nor has it been visible in the finished quilt. I do all of my own quilting, however, either on my domestic or my midarm frame setup. It has not been a problem at all on my frame setup, but maybe it is a concern if you send the top out to a professional longarmer. I would think their setups would be better than mine, but maybe they are more sensitive.
It may depend also on whether the quilt will be a "show" quilt or a family quilt. I make only family quilts. Perhaps having twisted seams in a "show" type quilt will make a difference, especially if it is getting a custom quilting job with fine details.