IF a good bond is developed between the subfloor and the thinset, the floor will be stronger in bending than without the thinset. Other than that, the thinset fills in any voids to help prevent flexing of the Hardibacker.
As far as the warrenty goes, I agree with tomh, it is probably meaningless anyway. Has anyone ever heard of anyone collecting payment for a subfloor failure??
Dodgeman