It is a PTU limitation and the procedure is there to cover single engine case. When in single engine the PTU is transferring HYD power from one system to another. The pressure transmitted by the PTU is 2500 PSI, not 3000 as the EDP, so the PTU is not capable of handling both gear and flaps at the same time. Following Airbus philosophy of designing procedures that are easy to remember and to follow, they decided that it would be better if they implement the rule of not operating gear and flaps at the same time in ALL situations, anticipating the fact that most pilots would forget about this in the quite infrequent case of single engine approach and landing.
The PTU limitation USED to be in the FCOM loooooooong time ago (like so many more things!), but got removed a while ago.