One of the advantages of having very non-technical customers, is that they could not care less that "OMG, it's stock bootstrap!". They just like that the site looks decent, and it certainly looks better than if I did everything myself.

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.