Heard this comment from a professor. It seems that the Spanish Government in the Philippines answered to the Officials in Mexico, instead of answering directly to the King of Spain. Thus, in practice the relationship between Mexico and the Philippines a the time was more like a colonist and a colony instead of being fellow colonies. How strong an argument is this?
The claim is technically correct (insofar as the Philippines' Captaincy General was part of the viceroyalty of New Spain) but Spanish colonial administration was so diffuse that it's wrong to argue that it was a "colony of Mexico." Sovereignty was held inviolably by the Spanish crown and the viceroy was a representative of those interests. Furthermore, the Council of the Indies still governed a lot of the administrative stuff. The Philippines wasn't any more of a colony of New Spain than, say, Puerto Rico. That's just how the Spanish colonial system worked under the Habsburgs.
It was pretty much impossible to get orders from Madrid to the Philippines without going through Mexico. That's why they did that but Mexico didn't exist at the time and it was New Spain.