Hi, Sara.
It's the duty of the countertop fabricator/installer to install the top to within tolerances of what you're installing for a backsplash. While installers LOVE installing thick 2 or 3cm backsplashes made from the same granite as the top because it allows for very easy installations that are fast-fast-fast....
They should ask you what you're planning for a backsplash as soon as they know you're not having them fabricate a matching granite backsplash. In other words, the moment they know you're not going with a thick backsplash that covers big air gaps on the back walls, they know they've got to be more accurate on the installation. It's time to get them back to do a little better job at fitting the top in place to reduce the gaps.
And no, there's not a real good excuse for not being able to do this, no matter how wavy your walls may be. There are LOT of countertop measuring tools from simple templates made with $10 worth of lauan plywood strips, to expensive laser measuring systems that are designed to allow fabrication in the shop to fit your walls and cabinetry to a reasonable degree.