Super Strike, does it stack with the enhancement bonus of weapon?
Invulnerability, does it stack with existing DR?
Enhanced Vision, does a dwarf's darkvision increase to 120 ft if they take the Darkvision Enhancement?
Gain Feat, at epic level, can it be used to gain epic feats? If so, then why would anyone use HrP on Energy Resistance, Fast Healing or Invulnerability?
Um, I think that's all the questions I have. At least for now that is.
The simple answer is "No." The more complicated answer is . . . more complicated. Then there's the really complicated option. If you don't want to go to the effort, though, just say No.
More complicatedly, if a character already possesses an ability (like Darkvision, or Damage Reduction) from a racial ability, determine the effective Hero Point cost of that power. The character basically has virtual Hero Points in that power. They can use Hero Points to gain more ranks, so in a way, yes it stacks.
However, the total of their virtual Hero Points and their real Hero Points still are limited to character level +3. So if, say, some race has the equivalent of 10 Hero Points of invulnerability, you cannot increase your damage reduction until you're at least 8th level. Before then, the level-based limit still restricts you.
For the sake of ability scores, any ability score modifier higher than +2 should be considered the equivalent of a super power. So, for instance, a Half-Dragon gets +8 Strength. The first +2 Strength is fine, but the next +6 is the equivalent 9 Hero Points. So if you have a half-Dragon superhero, you'd have to be at least level 7 before you could add more HrPs to your 'Heightened Strength' power.
The really complicated way has you discard all 'races,' and just create all their powers and bonuses via Hero Points. You'd want to maybe allow characters to take a -2 penalty to some stat and gain a 3 extra Hero Points at first level. Just a thought.
And as for Epic Feats, no. I think someone on this board, who actually owns the book, suggested a cost of 4 or 8 HrPs per epic feat. I don't own the book, so I couldn't suggest anything to you.