How thick should the seam coat of thinset be for Hardiebacker boards in a tiled flooring application?
I think you will be fine.  As you pointed out, the thinset under the tile will offset any uneven bump in your subfloor.  An even comb of thinset isnt required.  whenever you press down the tile and level it, the thinset will move under the tile to compensate for any bump.

Usually i only put just a little between the hardiboards just to fill the gaps.  Having a perfectly flat subfloor is not necessary.