That early? I'm not so sure about that. In 1600, there was a tenuous connection at best between Spain and the Philippines/Japan. Before claiming "they're going down," look at a map. Look at the distance between Spain and the Philippines. Now look at the distance between Japan and the Philippines. At that point in time, ships were basically rattraps that had no guarantee of making it around the world. In the early 17th century, there were very few Spanish soldiers on the island, they mostly made us of locals and the divide and conquer technique. If Japan really sets its mind on conquering the Philippines, what's Spain going to do? Shake its fist and write angry letters from the other side of the world until Tokugawa gets scared and runs away? Launch an incredibly expensive expedition across the world and hope that enough manages to keep itself from sinking to fight against tens of thousands of Japanese (and keep in mind that although Japan didn't have
many cannons or guns, it did have them, could capture more from occupied Manila, and it's not like the expedition would be able to bring a massive amount over) while the Japanese have a year, minimum, to prepare? Or would it ask permission of France, the Holy Roman Empire, Russia, and China if it could please send an army through their borders, then swim across the Sea of Japan and march on Tokyo that way?