IIRC the Dutch and ABDA did not recall or consolidate their farflung forces into the Soerbaja Redoubt. Hence why the designer included political points...
Actually, I don't think that is the design intent. Political points are intended allow you to move units to ANOTHER region, not between islands in your own area. I suspect that if you assign to a distant command you will not gain benefits from that HQ until you move nearer to it - and you will lose benefits from the one you used to be assigned to.
Also, I believe units DID move between islands. The Philippine Army was raised to defend its local districts. But when war seemed to be coming, fully HALF (3 out of 6 divisions) in the Visaya's were moved to Luzon - and ultimately ended up in the "Bataan redoubt" - exactly as you think didn't happen on Java.
In a game, why could the allies NOT choose to move things to the Soerabaja redoubt? Would it be a bad strategy? I myself see a different strategy - start up in Sumatra defending Palembang - and fall back across the strait into Java - then down the island chain to Bali, Lombok, Flores, fighting all the way. Being a modern soldier I am trained to retreat rather than stand and die before a superior force. It is not clear that this would work well - but why not allow a player to attempt it? Is it the designer's place to FORBID reasonable strategies? I think not.
Frankly I think the restrictions of restricted commands are far too severe - and very ahistorical. NEI and Philippines have actual dedicated fleets - and it is preposterous IMHO to say they cannot move troops. How did troops ever get to those distant points in the first place? It is also dangerous to move them - their ships and planes might be shot at - and slow movement across straits might easily be overtaken even by a slow task force. It is one thing to say "there is no railroad across these straits - as there is between Kyushu and Honshu (by tunnel)" and another to say they cannot move even with weeks of warning. I am afraid to mess too much with the command system until I understand it better.
So I believe this mechanism is a small step in the direction of giving the Allies more flexability in the defense (up front) - and Japan later on.
Upon analysis, I find there actually were places on the map where movement across water barriers is allowed - including the amazing Yangze at Nanking - between Kyushu and Honshu - between Shikoku and Honshu - between Hong Kong and the mainland - between Singapore and the mainland. I note a pattern to these cases: movement is fast and easy ONLY when there is a bridge/causeway (singapore), tunnel (to Kyushu), a major ferry system (Hong Kong) or a minor ferry system (Shikoku). So I will follow this procedure - and add a still more limited case - one where there is NO communications but a narrow barrier (as in a couple of cases in the Visayas). To cross with no aid what amounts to a river is correct for those cases. Otherwise, we will restricte movement to the sort of communications that exists - in most cases it will end up like the Shikoku Case - very slow compared to a railroad or highway connection. This means that troops can move between Seattle, Victoria and Vancouver - but not like they are driving - for example. Hawaii is a case I may ignore: it is not a restricted command area, and adjacent ports do feed supplies automatically. Troops can fly or sail on real planes or ships, so I see no big reason to mess with the map there for a marginal ferry service.
Other terrain corrections are adding two points in India, two in China, one in Russia, several in the Philippines, and maybe some other cases. The Russia case is at the mouth of the Amur - to solve a supply problem. The Chinese cases are also to solve supply issues and create real air bases - including a famous one. India needs the bases it really raised its air force at. I might add Saiki - the NE hex of Kyushu - but maybe not this round. Japan is pretty well organized with that one exception - and a need to ferry to Hokkaido form Honshu across the Tsugaru Straits.