Hmmm, the Dutch East India Company (f.1602) was based out of the Dutch Republic (independent from Spain in 1581, though not recognized by Spain until the Treaty of Westphalia in 1648). The Spanish Netherlands (Flanders+) did remain under Spanish and then Hapsburg control though. So the VOC existed outside of the Spanish empire and was a private (albeit state sponsored) colonial enterprise.

While Spain was interested in Indonesia (or the Spice Islands at least) and did make attempts to establish themselves in the area (Loaísa in 1526 and Saavedra in 1527) the Treaty or Zaragoza effectively carved out Southeast Asia as part of Portugal’s exclusive zone. Spain generally respected this in terms of territorial claims until establishing themselves in Manila thanks to Legaszpi’s voyage in 1565. Despite claiming Manila for Spain, their possession of the city, much less the surrounding hinterland, was fairly tenuous for the next century with the near constant threat of rebellion, attacks by Sultan Kudarat, Lim Ah Hong, the Dutch, or the British (who occupied it in 1762). Remember, the Philippines was technically a colony of the Viceroy of Mexico and therefore only nominally under crown control (consider that Manila was much closer to Mexico than Spain). That is to say, Spain was far too preoccupied with holding on to the Asian entrepôts it had to undertake any effective expansion further into Southeast Asia.