(Abhi)sankhara are the cause for all dukkha, because the sankata that a beings creates via abhisankhara will bring only suffering (in the long run). That is sankhara dukkha.
The question remains, why those two extra categories of dukkha (dukkha dukkha, viparinama dukkha)? Is it because not all vipaka is based on (abhi)sankhara of that certain being but based on conditons in this world? The world is made by sankhara/sankata of uncountable beings, thus a single being will experience bad vipaka based on the result of all sankhara (which we call “planet earth”).