Sewgood, YES custom quilting can be very much more expensive. Doing an edge to edge pantograph is pretty much just following the lines on the paper with a laser. But custom quilting means the person is guiding the machine completely. No guidelines, no pattern. It takes a lot more time.
Often, professional long-armers will have set prices for various pantographs. They know approximately how long the stitching will take and charge accordingly. However, if they are asked to do a custom piece, the set price could be by the hour. It is best to ask about rates and get some sort of ballpark figure before agreeing to custom work. (How do I know this? I have a friend who didn't ask and was shocked when the final bill came in. It was more than double what she was used to paying for edge to edge quilting. And it was too late to negotiate)