So the consensus seems to be, either they go to England, because the English were strong in the region, or they go to Spain--either switched directly to Spanish control with any Dutch present in Indonesia either submitting to Spanish administration, presumably from Manila, or fleeing or being kicked out and replaced by Spaniards or possibly allied/subjects such as the Flemish or Burgundians (but reporting to Spanish authority); or the Spanish, in order to achieve victory in the Lowlands, offer concessions to the Dutch if they submit, and among these they keep their acquisitions in Indonesia--but again, they are doing so as part of the Hapsburg empire, so ultimately the islands would be colored on the map as part of Spain.
Another thing to consider in this is that the position of England would be drastically worse in Europe if the Hapsburgs, at any time, manage to impose their kind of peace and order on all the Lowlands. If they do that, they have a prime position to attack England itself from--see Garrett Mattingly's The Armada. As late as the actual expedition of the "Glorious Armada" (as the Spanish-speaking world still ironically calls it), 1588, Alexander, Duke of Parma, attempting to conquer the Netherlands, was of the opinion that if he could only get the investment King Philip was blowing on the fleet, he could handily complete the subjugation of all the Lowlands, and from there Britain would be very vulnerable--if only he had control of at least one good coastal ports and didn't have to deal with the Dutch naval forces, which conditions would be met by securing the European coast.
It might be that Parma was still a bit overoptimistic about the possibility of getting a substantial Hapsburg force onto English soil, but certainly this would be more cost/effective than trying to do so from Spain! Actually, the plan of the Armada was merely to secure the sea route for Parma's troops to come over from the Spanish Lowlands anyway--but in the event, Parma held no port from which he could sail so even had the Armada prevailed at sea over both English and Dutch fleets, the invasion force would not have shown. But clearly had Parma already held the entire coast, thus cutting off the Dutch component of resistance as well as securing the best embarkation ports, assembling sufficient naval force to punch through isolated English resistance long enough to secure a beachhead there would have been much less of a problem. Perhaps still a more formidable one than they realized, given the performance of the English ships against the Spanish OTL, but the threat to Elizabeth would have been severe.
Mainly because a Spanish landing in any force would have faced a rather weak and inexperienced militia (the best English forces presumably would have been made casualties or captives during Parma's investment of the Lowlands) and even worse, an England of uncertain loyalties. With any political savvy at all, Parma could rely on an uncertain but even at minimum substantial defection to the Catholic side if he could offer them a banner of some force to flock to. Again, this might fail to prevail but the threat was such that Elizabeth would have to reckon with a worst-case scenario for her, which would be grim indeed.
Thus--if only Parma got his way, and succeeded as he projected he could given the full backing of Philip, not only could he secure the entire Netherlands for the Hapsburgs, he could largely eliminate the English threat without even having to actually follow through on the invasion, merely by the strategic menace the mere possibility of such an invasion posed. With the fall of the Netherlands, and the concurrent collapse of the Huguenot cause in France, England would suddenly be terribly alone as the only surviving Protestant resistance to Spanish domination of the whole Atlantic coast, and terribly vulnerable any time the Spanish monarchy felt it was time to swat a sufficiently annoying fly.
Under those circumstances, the probability that the English would be daring enough to seize Indonesian assets from the receivership of a triumphant Hapsburg colossus seems rather lower to say the least. One need not underestimate English defiance and the possibility that loose cannons on the other side of the world might dare deeds that the Queen in her prudent wisdom would forbid if her writ could only prevail in a timely manner over such wide seas, to foresee the whole thing ending on the whole poorly for the English East India ventures.
It might be that, in punishment for these and other provocations, Philip in due course does authorize and fund the Enterprise of England, from Lowlands bases under Parma, and his ships do manage (with some considerable loss, probably far more than they reckoned with) to cut a path for an invasion army, and there are risings for the Catholics that weaken English resistance--and yet the English might prevail on their own soil, rally at sea and cut the Hapsburgs off from reinforcement, kill or drive into exile any who overcommitted to the invaders while conciliating others who vacillated, and the triumphal miracle at sea of 1588 might in this timeline be transferred, at even greater cost of English blood, to some later year on land and at sea, and the timeline resumes the forging of a patriotic English identity that OTL the defeat of the Armada had so much to do with. And yet even in such a scenario, it seems clear that English ventures overseas would be terribly vulnerable and likely to be trimmed back rather than to advance boldly.
Or of course Parma could, with the aid of Catholic Englishmen, succeed in his venture, capture, kill, or drive into exile Elizabeth (and where would she go?) and then the English ventures overseas as well as the Dutch fall into Hapsburg hands, whether deeded over to the Spanish administrative machinery or under a compliant Catholic monarch, remain nominally English--but de facto part of the Hapsburg system anyway.
Basically, if the Netherlands fall, Western Europe as a whole falls, and everything overseas becomes Iberian-controlled (I believe at this point Portugal was also under Spanish control, and if not how long would they remain independent under these circumstances?), except insofar as the chaos involved gives locals the opportunity to oust the European foreigners completely.