This is the answer I got from Flynn about a month ago:
"It [ThemeFrame] will use the same layout technique and many page elements will have the same ID's and class names but you won't be able to import settings from Atahualpa."
Once you've manually set up one ThemeFrame site to your Atahualpa settings, you can then import that into your next Themeframe site. So it's a one-time problem, as I understand it.
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