In the background of some GDC slides there was the Destiny map with 'Puerto Princesa' and 'Thumb Peak' (in the top left) written on it:

https://www.dropbox.com/s/89inp4v23szbpqb/GDC screen - puerto princesa.png

Do you think this is enough to confirm the last city is in the Philippines? And any thoughts on why Puerto Princesa?

A quick wikipedia search showed that exact picture, only altered in color and shading. It is a 1904 map of the port city and the surrounding landscape. Seemed a little lazy on Bungie's part, right? Hahah

Also, the screens with all the guns from the GDC have a faded map background, I believe it is the same picture but cannot confirm at this time.