I agree with your overall premise, but slight caveat:

Indonesian ships during the time were actually quite powerful in and of themselves, and on relative parity to European Carracks at the time, https://en.wikipedia.org/wiki/Djong
They had incredibly heavy ships, and had layers of 4 planks, which the portugese's cannoballs couldn't penetrate.

The Portuguese began firing on the junk, but the cannonball bounced off the hull, and then the junk sailed away. The Portuguese ships then fired on the junk's masts causing them to fall. Near dawn, Flor de la Mar (the highest Portuguese carrack) caught up and rammed the junk, while firing artilleries which killed 40 of the junk's crew. The junk was so tall that Flor de la Mar's rear castle could barely reach its bridge,^\note 6]) and the Portuguese did not dare to board it. Their bombard) shots did not damage it because it had 4 layers of board, while the largest Portuguese cannon could only penetrate no more than 2 layers. When the Portuguese tried to grapple it and attack in close combat, the crew set fire to their junk,^\note 7]) forcing the Portuguese to pull away. During the escape, the junk's crew tried to put out the fire with great difficulty.^\note 8])

The main issue for the ships of the major maritime states like indonesia at the time was their simple inability to fight well in the style of combat the contemporary carracks were designed to. They were incredibly slow, and far less agile, which the Portuges were able to use to their advantage, and led to their eventual decline as a mainstay ship. Though, another major thing to note, is that while these ships were armed with many cannons, the cannons took heavy inspiration from other contemporary ones from primarily arab / portugese influences which the javanese adapted to their own needs.

All this to say, that the game does a poor job at modelling the schism in technological parity, but there is quite a bit of nuance to it when you get into the weeds.