To the contrast, the only way to go. When tourists behave like a disorganized flock of sheep, then every bureaucrat jumps at the opportunity to introduce a skyrocketing 'permit'. On which the bureaucrat can only win, cannot lose. He gets money out of nothing, also when local people suffer and the total number of tourists plunges. If tourists fight back, the bureaucrat will stop, because he (or his superiors) might not like bad publicity, and the money is uncertain.
I visited Komodo 3 years ago. It is a large island where the 'tourist infrastructure' consists of one pier, 2-3 buildings and few dirt paths covering a small part of the island. There are mostly boat tours coming for a day visit, and the main interest is snorkelling for 1-3 days. All is done by hired local boats, which benefit local people. It is one of the places least suffering from the mass foreign tourism I know of. However, I saw the advertisements of an upcoming luxury development, apparently aimed at rich Indonesian people wanting a second house.
The Komodo dragon occurs also in parts of Flores, despite its name. It was easy to see because five huge individuals were sleeping in the shade of the cantina building, which fish leftovers were probably be the best food source on the islands. But I would hardly call it a must-see animal for a normal tourist.