While the Philippines itself might be "an inconsequential archipelago", its conquest was not. You are talking about lands halfway around the world but literally in China's backyard. That's huge I think.
Imagine for example China conquered Cyprus or Corsica!
After 1500AD, Europeans positioned themselves as being able to credibly threaten any non-European nation while being safe from being threatened by them in Europe. Only Europeans and quasi-Europeans such as Ottomans could threaten other Europeans.
Psychologically, this was a major turning point. Because from that point on, Europeans actually could see that they had reached superiority to non- Europeans in their reach and ability to project power.
No.
Yes, my country is a symbol of European dominance. For all that that has lasted for 400 or so years, if you include the USA.
But no, we were basically the ass-end of the Spanish Empire and the periphery of the Chinese and Indian spheres of influence. Our region is more the Balkans to the Austrians and Ottomans and Russians than anything. And had Koxinga lived longer, perhaps we would see a maritime Celestial Empire of the South spread across the Malay archipelago instead. Or if a few lucky things happen, and Bolkiah's sons build a new and Muslim empire on these islands I call home.
This Spanish conquest only happened due to the Christian desire to push out the infidels made large, mixed with the desire to trade with China and lucky events that saw the fall of two empires (instead of simply vassalage which could be thrown off).
None of this would have happened if, say, Islam is butterflied away, or if Christianity is. None of this would have happened if, say, Egypt found itself an expansionist monotheistic faith and found itself less broken by the collapse of its neighbors, leading to other faiths and other nations. Or if Indochina's river civilizations started early, overtaking the north and east, founding a civilization which could spread from Madagascar to the Andes.
There are countless possibilities and paths, and though geography makes some possibilities somewhat more likely, it does not mean anything when time and chance happen to all. Especially when we only have one point of reference, which obviously favors Eurocentrism for good or for ill.
PS - And if OTL shows the norm of Eurocentric TLs, then it's almost certainly for ill.