In my experience, the fighting comes in when the designer (who generally has less understanding of the Bootstrap modules' intended roles) extends an existing UI concept that came out of the box. This is a perfectly reasonable ask on their part- it's a component on our site, why shouldn't we be able to customize it?
A specific example: Bootstrap expects dropdowns to be unordered lists with anchors as the top-level element, so having a fixed-position header as the first item while its children scroll is difficult. If this has been our CSS based on our markup, it would've taken fifteen minutes, because we could have gone in and done a bit of basic surgery on our module, making it more flexible. (This may not be the best example, but that's the general idea.)
A specific example: Bootstrap expects dropdowns to be unordered lists with anchors as the top-level element, so having a fixed-position header as the first item while its children scroll is difficult. If this has been our CSS based on our markup, it would've taken fifteen minutes, because we could have gone in and done a bit of basic surgery on our module, making it more flexible. (This may not be the best example, but that's the general idea.)