Internal piping cannot be taking into account in APV (and more generally, no internal part is covered by APV).
AutoPIPE can only model an internal projection radially in line with nozzle itself. But this internal projection should be only used as additional reinforcement for the opening. It is not intended for designing an internal piping. But you should take into account with nozzle loads the loads the internal piping will have at the nozzle wall. The forces and moments can be hand calculated for steady state conditions. Dynamic effects (like sloshing of fluids, earthquakes, etc) may be a bit more difficult to come up with the loading however.