People find all kinds of different ways to charge for longarming, but it all comes down to trying to get a decent wage for the time put into the quilting. I think the charges are set up the way they are in order to make the final cost more palatable (and understandable) to the customer.
I don't think most longarmers trim the quilt without an extra charge, and many quilters wouldn't want the longarmer to do that anyway since the method to be used for binding can determine how the quilt should be trimmed. I'm not sure what they mean by squaring, whether being sure it's square on the frame (which should be done with every quilt) or actually trimming to make it square before or after quilting (which should have the customer's approval first).