Bootstrap is like any other framework; it provides an expedient way to quickly construct your website. A person can be an expert in Bootstrap without really having a comprehension of how CSS or HTML works.
It’s not unlike jQuery in that regard… understanding the framework but not the underlying language.
I’m not sure I really share your umbrage though. I don’t think it is inherently wrong or bad for the companies you referenced to demand certain practices, including using Bootstrap. Perhaps they prefer the use of Bootstrap for consistency across designs? Perhaps they know that their service will need elements like alerts, tabs, carousels, etc… and as Bootstrap provides all of that it makes it an ideal way to get things done.
As much as you dislike that they are limiting you by forcing Bootstrap, aren’t you limiting yourself by treating Bootstrap like it is always going to be the wrong choice?
If you have specific concerns as to why Bootstrap might be the WRONG choice for a project I would encourage you to bring that up in a meeting with whomever your point of contact is for the project. But if it’s just a matter of “I don’t like Bootstrap because; reasons” well… if I were in charge of the project I would let you know politely that your issues with Bootstrap are not my concern, and that you would be advised to build a bridge and get over that problem double-quick :)