There's a reason people like opinionated CSS frameworks. They save a
lot of time which means customers save a lot of money, I can bet you my government which isn't swimming in money right now would not have the same opinion. Completely bespoke design is great but it is also a lot more costly for my client. There's also a basic usability heuristic of following the standard, by following a site structure the users are familiar with, it's easier for them to use it and I think that, coupled with design trends everyone wants to follow at the same time (see what happened with flat ui, which is all the rage right now despite creating poorer interfaces in my opinion), is the reason why many websites look similar and not because of bootstrap.
I also don't think that bootstrap is that hard to change, but maybe I'm just used to it. The upcoming Bootstrap 4 addresses some of the issues I think.
That said, there's a lot of good stuff in the government's document, it's well worth the read.