Can someone with over 1,000 karma start replying to a fresh comment before it's endorsed? Or will the reply link not be there until it's endorsed? If it's the latter, I'm worried that this might stifle the (admittedly rare) back-and-forth discussion between two experts, such as tptacek and cperciva. People who want to reply probably won't sit and wait until the reply link is active, and since replying to a different comment than intended is taboo, they're likely to say nothing instead.
That's a minor concern though.
EDIT: Also,
Since I'm going to check out of HN at the end of this YC cycle,
If I'm reading this right, does this mean you're going to leave HN entirely? I'm sorry to see that happen, but I understand why you'd need to.