Thanks for the reply infoworks. I've since reviewed the application and quote:infoworks said:You apply to the country of your passport, so, yes Aussie Expats are eligible, but you apply thru Immi in Oz.
"Hong Kong Permanent Residents note...
If you are an Australian citizen and you are also a permanent resident of Hong Kong please be aware that Hong Kong is currently not granting pre-clearances to foreign APEC Business Travel Card applicants who hold Hong Kong permanent resident status. This means your card will not be valid for entry into Hong Kong.
This should not present a problem, however, as ABTC holders use the permanent resident lanes at Hong Kong International Airport, which you are eligible to use anyway if you are a permanent resident of Hong kong.
If you prefer to have a card with Hong Kong included on it you can apply for a card through the authorities in Hong Kong, by virtue of being a Hong Kong permanent resident."
This implies that Australian passport holders with permanent residency in an APEC country have the option to apply via Australia immigration OR their "permanent residence" country.
However as a Japanese resident (and not permanent resident) I am limited to apply through Australia.