And: Bootstrap is not intended to be used "as is" in every case. It's supposed to give you an quick start, something you can extend and customize as you see fit. It does a terrific job at that.
Having a good enough default means I can spend my time improving the product, rather than worrying about something that neither the customers nor I care much about as long as it's good enough. And stock bootstrap very much is - that's one of the things I love so much about it.
With the flat design stuff, now I'll have to think about it, look for different solutions like themes, or maybe just going for it and hoping it's not a problem, and generally spend time not making our ebook conversions better.
Ultimately, it's not that big a deal, and I'm still way better off than without bootstrap, but I do consider it somewhat of a regression.