There have been several desirable features of Atahualpa that I discovered after several days of tinkering, and I may never be entirely clear on which functions come from Wordpress, not BFA.
For that reason, it seems like I should run an idea through this thread before making a mess over at the "request for features" column.
That said, I would like to have separate comment threads from certain pages activated from the page menu bar, but not all of them. Some method to exclude certain pages after activating "Allow comments on "Page" pages, too?" would work.
In my current confused state it seems like I could accomplish the same thing, only better, if we could assign new posts to a specific page, which would then become the new head of a separate thread. But that seems like it might require a WordPress revision.
Could someone straighten me out here?

And BTW, is there going to be a new program called "Themeframe" or a new Atahualpa rev 3.3.4?

That'll be integrated in 3.3.4 which will come within a week. After that I'll post a Themeframe update on themeframe.com

Could you explain the difference from the perspective of helping us decide which program to use, or is Themeframe going to replace Atahualpa?

They will exist side by side, Atahualpa is here to stay and will keep getting updated, maintained and improved. Themeframe will be more polished, with check boxes and radio buttons in addition to the raw text areas Atahualpa has. A few things under the hood will also be different. Starting from scratch gives me the opportunity to lay out a few things differently this time. Atahualpa will be more polished than it is now, but not as polished as Themeframe.