I think Koxinga would be butterflied in that POD.If Magellan's course had taken him a bit to the north, he might very well have landed at Tainan instead of Cebu. In which case he would have met Chinese merchants right off the bat. And Taiwan, not the Philippines would have been the country Spain would have wanted to get it's hands on. Not that it would have stopped the Spanish from taking the Philippines too.
Nor would Spanish rule of Taiwan have stopped a) Koxinga from taking it from the Spanish and b) Koxinga going al the way into the East Indies--perhaps all the way to Makassar and most of Borneo, forcing the Spanish back to the Moluccas and the Dutch back to Java and points west.
No, Koxinga would be butterflied because Magellan lived 100 years prior, and a century of butterflies would likely get rid of Koxinga. It might even get rid of the formation of any Jurchen/Manchu state and get rid of the Qing.How and why would Koxinga be butterfiled? The Manchu are still conquering the Ming. And still taking their time about the Southeast of China.
You don't need to go back to Magellan for a Spanish Taiwan. OTL the Spanish established forts and trade posts on the island starting in 1626 and lasting until 1642 when the colony fell to the Dutch. All you really need for a Spanish Formosa is to have the governor of the Philippines willing to commit the resources to properly defend the settlement and uproot the Dutch from the South. It's not like there isn't an incentive to do so either; the Dutch were a constant threat to the Spanish/Portuguese trade through Macao so Spain would have a significant interest in taking all of the island.