Fair enough.
I don't see any contradiction there. The Dutch East India company was important for the Netherlands. It led to the rule over Indonesia, but that doesn't mean Indonesia was important before that point. Indonesia would likely represent their pre-Dutch eras.
The naval trade aspects are important. However, I had thought before this expansion that Portugal would be less likely than we would normally think because it would be hard to find something to separate them from England, the Netherlands, and Spain. From the look of things, Firaxis succeeded admirably. It's possible to think of something else for Indonesia were they to want to - especially because their UU and UB/UI would likely have very little in common with Portugal.
I don't know enough about Indonesia to make a truly educated guess, but how about:
+1 happiness for each city settled on the coast. Extra food for trade routes between your own cities.
That would represent the archipelago nature of Indonesia and the fact that it's one of the larger populations in the world. Their UB could represent their cultural aspects without much difficulty.