score:3
So there turned out to be a rather pedestrian reason for my problem -- I was looking for seasonal April flights in November, so they weren't loaded into the system yet. But handily enough, this Japanese site shows future schedules as well, and a few months later, they show up normally in ITA Matrix etc. (At least the AE flights, that is; GE may not be running those flights in 2014.)
On the downside, China Airlines at least here in Sydney refuses to book them, you need to deal with Taipei directly. Worse yet, there are no combination CA+AE flights, it's full-price TPE-ISG at around US$400 one-way (or ~US$700 return) or nothing. So we ended up booking our flights via Tokyo, which makes no sense geographically, but comes out a lot cheaper thanks to the JAL Visit Japan fare that offers any sector in Japan for ~$100. Sigh.