I've never used out of the box bootstrap because of all the reasons you mentioned. I use them because I like the css class naming conventions. It makes sense to me and I use it across all my custom css too. But I do use the scss and cherry pick the parts I need for a specific project. In my case it's almost always just resets and grids and navs. Variables make it so I'm not overwriting a bunch of their code and I get very non-bootstrap looking websites.
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I've never used out of the box bootstrap because of all the reasons you mentioned. I use them because I like the css class naming conventions. It makes sense to me and I use it across all my custom css too. But I do use the scss and cherry pick the parts I need for a specific project. In my case it's almost always just resets and grids and navs. Variables make it so I'm not overwriting a bunch of their code and I get very non-bootstrap looking websites.