GREAT QUESTION Chris...diving prices in Australia in general are ridiculous...highest in the world easily, but these two take the cake. Regarding distance that's being mentioned...Navy Pier is a SHORE DIVE, yet you'll get charged close to $150 AUD for one dive, 2 dives on the Yongala are about $240 AUD, not as bad relative to the Navy Pier, but still more than you'd pay anywhere in the world. And while Townsville is a launchpoint, its not the ideal launchpoint...that would bein Alva Beach, far closer that Townsville and the price given is quoted from there. For the Navy Pier I know, at least when I did it, there is only one operator given the concession one time, so thereby I'm sure they can charge nearly what they want..and they apparently do. I really don't know why diving prices in general are so high In Australia...Navy Pier might be the most extreme example but they are high everywhere. Australia has so much great diving...it's so much more than the Great Barrier Reef...it's too bad it's not affordable.
While all that said, they are 2 FANTASTIC dives, two of my favorite in the entire world and, despite the cost, you just can't pass up doing them.