I expect that in practice, that's what's supposed to happen. But the only way you can be sure the reservation goes through is if you make the payment directly to the hotel and they then pay the commission to the tour operator. In practice, I think the tour operators block book the rooms at a discount and then sell them on members of the public. Even if the hotels insisted that they are upfront by the tour operator, this would provide no guarantee of a room as the tour operator could (in theory at least) book each room several times over.
I guess the only protection is to either book directly with the hotel or only book through fully bonded tour operators. I don't know if multi trip travel insurance policies provide cover against a tour operator defaulting, but maybe some of them do.