It comes on top of it. While the HA built-in mechanics affect raw damage, this affects final damage so it's not that bad: less damage reduction vs heavy armor and more vs light armor, while reducing raw damage is the opposite. On the flip side, HT feels quite accurate at level 35. The damage cap doesn't affect horses, so you can still hunt them (I was doing 30-40 damage with only +3 throwing spears and 5PT 4HA).
With all of these large changes, I completely forgot about speed bonus. I may bring the topic up but don't get your hopes up, lol.