I'm probably opening another can of worms with this post, but while I charge by the sq. inch, I also will tack on an additional $15 for every 15x15" space of dense fill--this is because it is so time consuming, it uses up a lot of thread, and typically the thread is needing to be a 100 wt. like Superior's Microthread--so it's not one I would typically be buying. I do many quilts for people that applique and they want lots of dense fill around their applique or embroidery.
I also think it's important to point out that there are so many different types of machine quilting that stating a hard and fast price for all quilts per sq. inch is very difficult to do. For instance, if I do a panto or FMQ Edge to edge, use one color of thread, the price per sq. inch is going to be less. If I do that FMQ, but now treat the borders differently (maybe even have to rotate a quilt which means unpinning and reloading)then the price goes up a tad. If I'm asked to do custom quilting with ruler work on all or most blocks, then the price goes up. And if I am asked to use two or more colors of thread, then the price goes up. Ruler work and switching out thread color is time consuming. I do know a couple of long arm quilters that have computer guided machines (mine isn't) and it's possible for them to record on the computer the # of hours involved in the quilt and one of them has switched to charging by the hour. She seems to be able to estimate the cost pretty accurately, too.