I know exactly what you mean.
The quilt in my avatar is done as I intend to do this next one.
The black is single layer.
While the top is waiting to be quilted, you are correct, the extra thickness is quite noticeable. However, once the piece has been quilted to the batting and backing, there is no noticeable difference in how it holds together.
The one thing I have noticed is that I don't highloft batting, in fact, I can use a flannel sheet for the batting ...
I think that because the pieces we have done so far are so much smaller than the simple sashing between my blocks in the avatar the problem will be greatly reduced, though it really isn't a problem at 10.5" as in the avatar <wave>