If you are using HDL can you not add a component (net_short) that has x_number of pins (depending on the number of shorts). Make the footprint a via and place all the pins on top of each other. Once the netlist is imported you will have to add some properties to the pins - NET_SHORT and to the symbol NODRC_SAME_SYM_PIN. But at least your net short will be in a pre-defined location.
I have attached a pdf file that shows this principle working except that the front end tool is Capture and the net short property can be defined in Capture and transfered to PCB.