As someone who does exactly this - building a website with Bootstrap or similar tools will get you 90% of the way there in terms of how closely your functional product matches its design. The remaining 10% requires fighting Bootstrap (since this is css, this means overriding rules). This is annoying and produces a fragile resulting code. Maybe it's a reason why the 90-90 rule exists. Instead, I choose to write exactly what's needed instead of trying to shoehorn in something to save time initially.
The shoehorning can come from designers who don't put things together using bootstrap components as their design language. Then the developer tries to do forbidden CSS alchemy and go from a Bootstrap component to the designer component. That's using an opinionated framework when your designers don't share the same opinions which often will make things more difficult.
Bootstrap and other opinionated frameworks are super handy when you don't have designs/designers though.
