The current regencies and colonial ones are..well mostly still continuing to exist, yes. However it has almost completely different borders, due to districts and subdistricts being moved around. It's why I really recommend using Robert Cribb's maps as the base, as it's accurate per the 1930...
I am an Indonesian, and this is accurate map for Tidore. https://en.wikipedia.org/wiki/File:Sultanate_of_Tidore_in_1800.png
Though it was more suzerainty, so a legal fiction. The administrative divisions used weren't even considering Tidorean's claim, except during 1898 where they created...
The thing is, the poorer the kingdom the less they have the ability to resist. The richer the kingdom, the more they are a great prey for the colonizer. It's like you're just
out of the crocodile's mouth just to enter a lion's lair. So poor Madagascar -> Colonized, rich Madagascar -> colonized...
Let's go to another country, Demak. Did the islamization of Majapahit happen? Yes. Did the coastal areas convert? Yes. Was a new Islamic kingdom created? Yes, Demak.
Now with a new Islamic kingdom, did that mean the population of the hinterland convert? Yes and no, Blambangan needed the Dutch...
SMH, I would argue the best situation for Madagascar is earlier unification and Islamization, which while they would still remain colonized, would be better pressed to remain intact politically. Similar to other native kingdoms in East Indies and India.