The reactor that Gates talks about (Natrium) uses sodium as moderator and coolant. In other words, the uranium fuel is submerged in a pool (literally, a pool) of liquid sodium. There are some pipes that circulate the liquid (and very hot) sodium to a separate place, where it heats up a secondary circuit of molten salt. That molten salt then goes on to heat some water and make it steam, which then drives some turbines and generate electricity. Or that molten salt can be left molten for a number of hours, as some form of energy storage solution.

So, the molten salt does not get in contact with the nuclear fuel in any way in this design.

There are other designs where this happens, and especially, there are designs where the uranium (or thorium) is itself part of the molten salt. Even Gates's company, Terrapower, has such a design in the works. But the Natrium reactor is not that.