diver dan,
I think it's a very intelligent move to create a new Capital City away from the hordes of fanatics & extremists. Start anew without the distracting masses of saboteurs of a huge city !

All very well to build a new city.

Can Indonesia keep all its disparate parts under one governmental structure?

Papuans are still being harassed and attacked.
It seems the latest trick is to throw a bag of venomous snakes into a student dorm:

https://www.abc.net.au/news/2019-09-10/west-papua-students-say-bags-of-snakes-thrown-into-dormitory/11495800

Can Indonesia keep all its disparate parts under one governmental structure?
Waverley,
With a population of 220 million my guess is it'll always be a massive challenge that Australians can't even begin to comprehend.
The snake episode is a wild one alright ! Still, burning shops & other property is no less heinous.
I've experienced those carpet snakes myself, very aggressive ! They can inflict severe infection, more so than a machete cut !

Good move in part of Jokowi administration to move the capital from Jakarta. It will help distribute development more equally to Kalimantan, while decreasing the burden on the overpopulated Jakarta area with 30 million people in its entire urban conurbation.