On the majority of cases, not true. The stink of a bootstrap is still there even if it's mostly over-designed. But that's not the point, the point is there's so many sites out there with just bootstrap - nothing else - and that is bloody horrible. Developers should stop inventing ways to be more lazy and just do what they do.
SASS, LESS, Bootstraps, insert_whatever_thing are just tools that ideally help to be more productive, but a few years in and you rarely see any raw code or from-scratch work. And they won't care either, because "it's more productive" is a perfect argument.
You seem to miss the point that many of those sites wouldn't have been launched in the first place if a way to make it look half-decent, fast, wasn't widely available. Making a website, especially a web app, takes some breaking inertia, if you've ever tried you'll know, and anything that helps you in getting it out is one step further from not launching at all. Given popularity, the design can be amended. A non-launch has nothing to amend, and is, if nothing else, a tiny loss for the web.