Just an update on my issue. The battery light flickered on and off for weeks, but the alternator was still outputting plenty of voltage (13.8v+) but in the last few days the alternator has started to fail completely. It now puts out between 11.8 and 12.8v and the battery light is constantly lit. So it seems to me like the flickering light can be an early warning that the alternator is beginning to fail, even if the voltages are correct.
I'll give Bansheebuzz a call tomorrow for a replacement.
Edit: Bansheebuzz is snowed under at the moment and doesn't have any upgraded kun26 alternators in stock. So he won't be able to supply me an alternator for a few weeks. So I went to see my local autoelectrician instead. He's a family friend and a good bloke. Knows his stuff and loves his Toyotas. Anyway, he advised me not to buy a genuine replacement alternator. Firstly they are very expensive at over $700 and in his experience they aren't particularly reliable. They also have the low output voltage issue which is well documented. Anyway, he sold me an aftermarket alternator instead. I'm usually not a big fan of non-genuine parts but he was adamant it's the way to go. He also said to avoid the alternators with the larger output that are available as the fusible link would need to be upgraded and it's not worth the mucking around doing that. Anyway, I bolted it in today and surprisingly it's pumping out 14+ volts at idle which is something even the upgraded factory alternator with the solid pulley never did. I would need to have the revs up to push the old one over 14v. So the output appears to be good. I guess the real test will be longevity, but it can't be much worse than OEM, and at half the price. So if anyone is interested, this is the brand and model.