Keep in mind I'm talking about major investments from 2 governments here, dockyards 16 years in construction costing 60 million pounds and having the largest drydock in the world, plus a railway running for thousands of km.
So what? You've built a major naval base in the back of beyond where even basic rations need to be transported in by rail or sea for thousands of miles. Great logistical planning there.
Also, will you care to tell us how you're going to convince all the civilian workers the base needs on even a peacetime basis to relocate to the ass end of nowhere? Bigger paychecks aren't going to do the trick, especially when you remember families are involved.
How would the Japanese outflank Darwin?
Try looking it from the RN's perspective for a change, after all they're the ones stuck basing out this foolish boondoggle. How are they, operating out of Darwin going to flank any Japanese aggression against Borneo, Malaysia, or the DEI?
Look at the map. Singapore sits on the "flank" of any Japanese thrust towards those goals as well as controlling the quickest route to India. Darwin, on the other hand, sits
beyond Japan's likeliest targets in southeast Asia. Any RN force based in Darwin is further away from the places it needs to defend, will take longer to respond to any attacks, and will need to pass through a limited number of passages between major islands thus giving Japan a better chance of detecting them.
Sounds good to Yamamoto!
Would Force Z sortie into the teeth of the Japanese operating from Indochina if it was based in Darwin?
Probably not because it wouldn't be able to get there in time to accomplish anything useful anyway and, when it did, it would have to be based out of Singapore anyway because the RN doesn't have a fleet train.
Singapore to Darwin:
Send Force Z quickly! Enemy troops transports have been sighted heading to Malaysia!
Darwin to Singapore:
Righto! We'll be there in four days, okay?
Singapore to Darwin:
Hurr Durr Derp Herp...
You've got this all topsy-turvy anyway. You're looking back with perfect hindsight knowing that Japanese bombers will easily sink Force Z while it's steaming on the high seas. The people at the time didn't know that, only a few barely even suspected it could happen.
They put Force Z and the naval base in Singapore so both could be
used against any potential Japanese aggression, aggression whose goals, targets, assets, abilities, and character they can only speculate about.
You're putting Force Z and the naval base in Darwin so that both can be
saved from the consequences of Japanese aggression, aggression whose goals, targets, assets, abilities, and character you know perfectly thanks to the historical record.
Your idea only makes sense from a 2010 standpoint as it "saves" Force Z and the naval base to perhaps fight another day. From a 1930-41 standpoint it makes no sense at all because it removes Force Z and the naval base from the very region they are supposed to be helping defend.