From the OP article:
As today’s U.S. Navy ponders how it might return to these waters in a future war against China, the lessons of Java Sea are especially relevant. Access to ports, the distribution of supplies and maintenance facilities, familiarity with the region, and effective working relationships with partners will all bear on the success of combat operations against the People’s Liberation Army Navy.
While the place was not predictable, the demise of the USN’s Asiatic Fleet, if it tried to defend territory, was predictable. It was a motley assemblage, IIRC, of one modernish heavy cruiser (USS Houston), an obsolete light cruiser (USS Marblehead), several obsolete four-piper destroyers, and a mix of obsolete (S-Boats!) and modernish submarines (two or three or four classes earlier than the Gato class). Yes, they were under-trained (an apt point the article made), yes they had had no experience working with what little forces the Brits and Free Dutch had, and yes there were poor repair and logistics facilities. But the biggest problem the Asiatic Fleet had was that it was too weak and largely obsolete to be meaningful opposition to the IJN's Kido Butai and far heavier surface forces. The Asiatic Fleet also had no meaningful land-based air support in the face of the IJN's and IJA's land-based air forces. They were a weak force positioned in the IJN's back yard.
IMO, the Asiatic Fleet should have been withdrawn to Brisbane or Perth immediately, US Marblehead and the four-pipers sent home "immediately", and the S-Boats replaced as soon as practical.