From Zamboanga city to the rest of the world
Backdoor- by definition, means a rear or secret entrance. In the Philippines however, this means illegal entry of goods/person to another country.
On the contrary, Zamboanga port is very much legal international entry/exit point , you will have to pay the international travel/tourism tax of 1620 pesos imposed my the Philippine government and you will have your passport stamped at the port.
Of course, you have the choice to go "backdoor" via sulu, which is only 2hrs by motorboat, but then again Malaysian coastguards are very efficient in catching illegals, so dare not!