First of all, I agree with those who point out, colonization is colonization, make no mistake about that. There are different kinds and degrees of it; given that a people observes they are surrounded by territories being grabbed by greedy foreigners who appear to be unstoppable they might well prefer to offer one set of these marauders a deal more tolerable to them then they are likely to get from the most ruthless of the lot, but that's making the best of a bad situation. I think we can take it as given that all peoples of whatever level of development prefer to be independent, if they judge they can.
Now, given that the Spanish were at large all over the world from the early 1500s on, the reason they did not attempt to gain footholds in East Asia or Indonesia was the
Treaty of Tordesillas, which was between them and Portugal. It was mediated by the Pope and from the point of view of the Papacy, the Spanish, and Portuguese, it excluded every other power from any territory outside of Europe. Thus the Spanish and Portuguese abided by it, though not without haggling. The Spanish colonized the Philippines in technical violation because that archipelago was clearly in Portugal's alloted sector, which however was by supplementary agreement larger than Spain's. From it they could hope to develop trade with China--which they did to some extent. But while intruding into Portugal's alloted sector they were clearly a good distance back from either the spice islands or the actual trade routes the Portuguese valued, and by being both generally scrupulous and specifically tolerant of specific deviations (such as Portugal's expansion of Brazil well past the original treaty line, or Spain's possessions of a few bases on the African coast) both sides could generally rely on the other leaving their central concerns--the Spanish American colonies; the Portuguese trade monopolies--alone.
Obviously as other European powers, mostly but not all Protestant, asserted their own interests in defiance of this Treaty they were never party to, eventually that became a dead letter. Soon the Dutch and others were well established in Southeast Asia, and meanwhile Spain as a world power was weakening compared to Britain and France.
But still, the French didn't get around to establishing their foothold in Indochina until the nineteenth century, and in the interim there were periods (at least one anyway) where the crowns of Portugal and Spain were united, so I suppose there might have been opportunities for the Spanish, based in the Philippines, to get to somewhere in Indochina first; they certainly had a much bigger population base than Portugal for colonial purposes.
To get into the question of just what opportunities might have come up you'd have to look closely at the detailed evolution of the Spanish imperial system, and meanwhile at the drama of Indochinese politics, and ask yourself just how intrusive a Spanish venture might get away with being, bearing in mind that not only were the native polities not completely helpless themselves, they could also take the risks of bringing in rival European interests to check or oust the Spanish. So I'd guess if they were going to come and stay, even in a limited territory, they'd better be very astute about it, especially as their power projection was constantly weakening relative to not just the English and French but also the Dutch, who soon had their own strong base in the region. By the time the French were interested and capable of their own strong-arm ventures in Cochin, the English were I believe strongly based in Malaysia and eventually Singapore, and had in fact at one time or another seized control of parts of the Philippines themselves for a while.
So unless one has a POD that involves the Spanish Empire having a strong comeback for other reasons, or the Indochinese venture proves a strong base for them, they'd always be at risk.
I don't see why the Spanish would be any better liked in Indochina than the French were; conceivably they might be more politic and accommodating considering their basically weak position but that doesn't sound like the Spain one knows from general history! If anything one has to anticipate they'd be more dogmatic and obstinate in trying to Christianize the population than the French were and I don't see any reason to think they'd be more successful at winning them over by sweet reason! Probably just as the French did, they'd successfully cultivate a limited number of converts to Catholicism, deemed with justice in many cases anyway by the Buddhist general populace to be mere cynical traitors to the proper local traditions, and favored by the Spanish as much for their dependency precisely because they were despised by the general populace as out of appreciation for their finding the true religion as Spain saw it. I don't see any reason to expect that the Spanish would respect and value these converts any more than the French did theirs, and even if Catholic, Hispanicized Indochinese did enjoy a better status among Spaniards than OTL Vietnamese Catholics did among the French, they'd still be a comprador minority along with the colonizers against a hostile majority.
The alternatives are either that the Spanish would enjoy a success that eluded the French in bringing the whole populace more fully into their system--and aside from the strength and dignity of local tradition I think all colonial powers more or less "failed" in this because none felt really motivated to try, enjoying both psychosocial and material advantages as they did by lording it over the natives as a "master race." By the time a liberal and humane conscience was reinforced by the pragmatic fear of losing control completely and enlightened colonialists might have sincerely hoped to fully integrate the societies, the colonized peoples had had quite enough of European hypocrisy and foresaw the prospect of gaining full freedom on their own terms. Again, I hardly think that an early and sincere feeling of ecumenism and restraint in enlightened self-interest was more likely to develop among Spanish colonialists than any other Europeans!
Or that the Spanish would rule with a very light and judicious, discreet hand. That seems scarcely likely either, and if they did, it isn't clear how it would bring profit to the Spanish, and the Spanish badly needed some kind of profit to enable themselves to protect their possessions. Without credible power to protect Indochina, the territory would at very best enjoy being sheltered from the rough and tumble of colonization by sheer diplomatic brilliance--and enjoy being left backward (if less run into the ground) as its more harshly colonized neighbors were perforce gifted with the vestments of 20th century industrial society.
The best case I can conceive would be if the Spanish protectorate somehow enjoyed a Meiji-like renaissance of industrialization on its own terms. But if they could do that, they'd hardly need Spanish protection, and they did need it early on, there is hardly any guarantee they'd keep to the Spanish orbit in gratitude! Nor is this a likely outcome by any means--and it hardly seems conceivable the Spanish would refrain from meddling in such central matters as local religion! A light Spanish hand would hardly be recognizable as Spanish!