Thank you, thank you, thank you all! You guys are just a big pile of awesome!
In reading through the responses, we were able to begin to separate the executive function issues from the content issues and compare those to her experience in regular classes versus this kind of inverted classroom. I can see that she's still learning to "lean in" when it gets tough (which is her experience in math this year), but that this particular class is like a perfect storm of mismatch (too much complexity, too fast, inverted class, etc.).
From this context, we were able to have another, more productive conversation with DD about the situation. One that moved us away from the knee-jerk perfectionist "this is hard, I can't do this" responses and toward some clarity.
It seems like she's still passionate about biology (writing the lab report was the most fun she's had in the class). She expressed a desire to find a different AP Biology class or study biology on her own through the videos she's already been working through. So that's a very positive sign.
She also pointed out that she had the same teacher in the middle school level version of the same class and learned a ton and loved it... but it was a direct teaching model (read the handouts, discuss in class, follow with a lab). And that she just felt lost without the in-class context. Not that I think students will always have the option of dropping a class that's a bad fit, instruction-wise, but that having it be your most challenging class isn't the best idea either.
So after some discussion, we decided on a swap. She could drop AP Bio for the next term, and pick up an online Intro Chemistry class specifically for gifted kids (in class lecture and Q&A format, only through skype). This class should be challenging, but the syllabus describes is as "when you're done with this, you will be ready for AP Chem or first year college Chem" so it's the class she needs to fill in that science gap. There will be regular homework and at-home labs (which can't be too interesting, but we could always spice them up a bit).
We took aeh's advice to structure this as a mismatch in teaching style coupled with bad timing, rather than "this was just too hard." We also made it clear that we expected the same application of effort through the rest of the year in math and chemistry. And finally, we said we'd look for another AP Biology option. One more year and that problem will solve itself anyway, because she'll be able to enroll in our local community college for high school level science (13 can't come fast enough for her).
Also HK, this:
"Without an interactive classroom experience, my DD tends to assume that her struggles with material are disproportionate and not shared by her classmates, who must have mastery while she is slogging through things. A flipped classroom experience like the one described would be a pretty toxic cocktail for my DD that way."
... is exactly what she's been expressing. "Everyone understands this but me." The fact that she's three years younger than everyone else in the class and everyone knows it doesn't help either. We don't see this same insecurity in her other classes BTW. In history (where again, she's at least 3 years younger) she's perfectly confident, even standing on a chair to debate a particularly tall opponent during a class exercise.
Thank you again. There is literally no one who DH and I can discuss this with IRL. Because the response is always "of course it's too hard, what were you thinking pushing her like that!"