In "The History of Southeast Asia: Every Year" by EmperorTigerstar, Maritime Southeast Asia was divided into many political entities. Even the mighty Srivijaya and Majapahit empires couldn't unify all of Sumatra and Java. Meanwhile, Mainland Southeast Asia kingdoms were bigger and less divided. What made it Mainland Southeast Asian kingdoms less fractured than Maritime Southeast Asia kingdoms.
I don't know enough about mainland SEA to make a comparison, but I wrote about why Indonesia had so many sultans here:
which touches a little on why there could be so many polities in what is now Indonesia.
I would also add that we should not assume that an empire is always one continuous land-based polity. Just because "the mighty Srivijaya and Majapahit empires couldn't unify all of Sumatra and Java" does not mean that they were small or fragmented, any more than just because in 50BC a small village of indomitable Gauls holds out against the invaders means that Rome is small and fragmented.
The video you link to shows that these two empires were massive. They may not have controlled their entire home island but they sure did control a lot else.
And, the areas they did control may well have been more valuable than the parts of their home islands that they did not. For example, a lot of maritime SEA polities focused on the coasts, which had valuable ports. A port does not look very impressive on a map, but it brings in a lot of revenue for whoever controls it.
Control of ports would also have allowed them control over shipping routes. This would have brought valuable parts of the sea under their control, which again is generally not reflected in any map.
I'd just like to add that Champa in central and southern Vietnam is also thought to have been a collection of polities rather than one unified kingdom, as the map shows.