Almost forgot the whole point of the mod;
The raid on Manila for career start is mostly just for fun, but the real reason is to get closer to the action and carry the war to the enemy without all the cruising back and forth. Asiatic career in stock game starts out okay, but being moved back to Java makes for longer distance travel, and once Java falls you might as well be based in Pearl than any of the Australian ports since the travel distance is about the same. This shot is from 1943 starting a career in Brisbane, if you're really determined to take an S-boat all the way to Tokyo it's possible by using the supply bases.
Fuel, ammo, and torpedoes only, neither PHANTOM 42 or SPECTRE 42 is much of a liberty base.

But they do have the advantage of being only 1500 or 2000 miles from Tokyo. No, Tokyo is a lousy liberty base too, American sailors not welcome there while the war is on. Can't blame them, bunch of US sailors on liberty would cause more damage than the B-29s ever did.