Update.

Booked the boat through a hotel (Bay View Gardens - nice and cheap place overlooking Labuan Bajo but not for anyone who is even slightly mobility impaired) in Labuan Bajo who arranged with a boat owner and passed the payment on (the Dutch owner's economic development philosophy). IDR 1.8mm for the two of us on a covered deck ex-fishing boat with meals and drinks for 2D/1N. A cabin boat (same kind of boat with a small cabin behind the steering room) would have provided a bit more privacy. As it turned out, it would have been nice for a few minutes during the evening (and overnight) rain storm but the tarps were good enough.

This of course did not include park admissions or snorkelling gear, or the transfer from LBJ. Overall, still a lot cheaper than what was being offered.

We flew on Sky DPS-LBJ which does accept foreign credit cards for online purchases and cost a bit more than the other 3 (~$100 p.p. per leg).