Why, do you think the pilot said "Hey, we're running out of gas", only for the plane itself to force him to fly on? No, running out of fuel is a pilot error. If you are referring to 2nd May 1943, the Spits shot down between six and ten Japanese aircraft for the loss of five Spits in the actual air combat, then five Spits then made forced landings due to running out of fuel. They had used too much from the long climb followed by dogfighting with the Zeros. On the plus side, the majority of the Spits that did run out of fuel were repaired and returned to service. I can find only two Spitfires at Darwin that ran out of fuel and were too badly damaged to be repaired. So, despite pilot error, the long-term effect on the defences was small. After the 2nd May 1943, the Spits carried drop-tanks and avoided dogfighting, which chewed up fuel, and were so effective that the Japanese made their last major raid on 6th July 1943, and abandoned attacks on Darwin by November 1943.
Your post said neither side could fly far over the Channel without running out of fuel. My reply was not intended to imply either the Spit nor the ME109 could have flown 500 miles, had a combat and then returned, it was to fill in the gaps in your knowledge regarding both Luftwaffe and RAF range capabilities by 1942.
And there were how many P-38s, P-47s or P-51s at Darwin? The Allied defence at Darwin was tropicalized Spitfire Vs and P-40Es. The Me410 could outrun both with 385mph top speed, could fly higher than the P-40 could, and was excellent for boom'n'zoom tactics. It had the firepower to knock either down in a single pass, and the dive capability to then speed out of range to make a safe recovery, necessary given its relatively slow climb rate (though still better than the P-40E). The problem for the Me410 as an escort was there simply was no Luftwaffe role as long-range escort by 1942. I was also faster than the Zero, by quite a margin, and had the advantage of a rear-gunner to warn the pilot of attacks from the rear. It could even have carried bombs to Darwin, dropped them and engaged or evaded the Spitfires at will. Did the Zeros carry bombs to Darwin?
Beaufighters shot down ME109s and ME110s on day sweeps over the Med and Desert in 1942, both of which out-perform the Zero. The Beau II with Merlins would also have had the altitude performance to come in above the climbing Spit Vs (and well above the P-40Es), allowing them to position for diving attacks out of the Sun. Maybe you should think more about the scenario before passing such quick judgement? To be successful, an escort does not need to shoot down every enemy interceptor, it just has to disrupt them enough to keep them from attacking the bombers. Having said that, any Spit V or P-40E that got in the way of a diving Beau would have been shredded by the Beau's cannons.
I didn't include them because there were none at Darwin.
It didn't whip anything, the RAAF pilots stupidly ran out of fuel. A properly flown Spitfire V Trop was more than capable of besting a Zero, and the Spit V Trop was pretty much second-rate by mid-1942, let alone by the time of the Darwin raids in 1943. Please also note that the Spits were tasked with shooting down the bombers, not the Zeros, and shot down more Japanese aircraft than were lost in the defence of Darwin.
Except for the Me410, the Beau, the Mosquito, and the P-38 at the time, and planes like the P-51B/D or P-47N much, much, much better later in the War.
You're on your period? That does explain a lot.