Yes, as long as the Pay Items are defined on an element, they will be computed in quantities. (regardless if they are in a reference file or the working DGN file)
No, the Pay Items must be defined on the elements/features in the working DGN file.
It depends on what the Pay Item is set as. There is a setting in each Pay Item that allows the either of the two different options. Under the Measurement section of the Pay Item dialog, there is a Mode option that allows the user to select which way the quantity will be calculated.