I have read that some LA quilters do charge by the hour, but, I've never met one!
I don't really find the 'caffeteria' style charges a problem. If anything, it encourages the person bringing the top to do as much of the work up front to avoid additional charges. For instance, it's my opinion that you should square up and thoroughly press the top before dropping it off.
I'll be curious to see other's opinions.
As far as renting out the machine, it's an expensive item and i wouldn't want just anyone using it. Also, there are liability issues.