For the simple reason that Macao and Melaka were able to get into the list seemingly smoothly (and it's really a mystery how they got in, especially if we apply to them the same standards we are using now in judging this tentative site), I see no reason in principle why Batavia needs to be left out. More importantly, Batavia was far more pivotal than the two during the age of trade, playing a most key role in the growth of the Dutch empire as a global superpower -- that's a fact that the East and West can easily agree on. It's history is monumental. While the accusation that "it lacks a cohesive area representing its golden age" is justified (it is not like Hoi An or Vigan, true), the evaluation is certainly not: Even with its stadthuis and Sunda Kepala area alone, an OUV can already be established (Bremen can attest to this approach). The fascination with the notion of "the more old buildings, the better" is getting more and more problematic and rather undynamic. That measure alone is not even a good yardstick in the valuation of heritage especially in Southeast Asian contexts.  

Another welcome alternative is to catapult Batavia/Old Jakarta to the spice trade route sites, a highly promising WHS nomination that Indonesia seems to be pursuing. This is an interesting website to explore: www.jalurrempah.kemdikbud.go.id 

I visited Batavia in Dec. 2018, and stayed at a hotel beside the old town square for two nights. Glodok can be conveniently discarded in the final nomination, in my opinion. I have yet to see the outlying islands.