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No. UK still controls Malaya. If Japan captured Malaya, then another Allied power recaptured it while Japan still held India, that power would then control Malaya and could build an IC there.
If a sub attacks a lone transport outside an enemy island with an airbase and fighters, is the transport automatically sunk, or does scrambling do anything to prevent that?
The fighters can scramble. However, since there is no defending destroyer, they can’t hit the sub. As a result, the transport will be sunk anyway.