Ultimately, let's be honest: we want the most number of people to be able to experience these things (I fortunately went to most of these places before the recent boom and I think they're wonderful) while ensuring that the cost to the environment isn't catastrophic. That means some people can't go. We can pick some mechanism but it will necessarily exclude some people. The money is the best selection mechanism because we can use it at pretty high granularity on preserving the thing that is bearing the cost, but any substitute that serves the purpose does just as well.
The key magic is that with money we can undo some damage. That's what makes it a useful thing to auction on.
Less wealthy travelers go at odd times, they live in hostels and have "worse" experiences.
The only difference in this case is that the country is also directly profiting from this demand.