I have wondered the same thing all along. And whenever I complain about the non-semantic nature of bootstrap use, people justify with that same, "but this is just to get started" argument. So that's what everyone says. But I don't think it's what anyone actually does.
I think if semantic markup is important, then don't use bootstrap. Once you use it, bootstrap will always be part of the project's DNA unless you do a true rewrite. But, to your point, that almost nevers happens.
