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Current I believe comments pay out when the original post pays out.
Then what happens currently with comments which are written after the payout for the article?

You cannot comment after the post's payout now. Note that, there is a second, 30 days payout in the system.

But with the HF proposal to make final payouts after 7 days - there will no longer be a 30-day second payout, right? So if the comments payouts are separate, they would also have final payout at 7 days. I'm assuming that no new comments would be allowed after original post payout then, but have not seen any wordage about it.

@merej99 (nesting limit)

Yes, after HF17, only one 7 days long payout period remains.

Since comments count as individual posts in the new system (as you have said, they have separate payout window), I don't see any reason why we shouldn't allow comments after the posts payout.