Reading throughout the comments and replies I’m sure you can come to understand how your vision of Bootstrap and the principle of Separation of Concerns is kinda wrong.
You keep defending your point of view, which is right and you should do so, but some things are technical, hence the right or wrong is pretty much decided by the thing itself. In the case of Bootstrap, which is a technical piece of CSS which is opinionated and yet semantically correct, the Separation of Concerns is respected.
The fact that you have to change a class name each time you want to change the layout of a single page is not an attribute to Bootstrap, it is a must-do of any web page, since you are talking about changing the single pages layouts you would have to scout through those 100 pages anyway, whether you use bootstrap or your personal CSS.
A smart solution which comes with backend rendered pages (PHP, NodeJS, Ruby, Python and others) would be to include headers and footers, separating the logic of the layout into smaller and more easely changable pieces.
To answer your question, you are not being too principled, you are just not getting the right meaning of the principle.
If you were to change that “col-md-6” in a few pages you would have to do it manually, true, which is bothersome, also true. But you would be doing the same if you were using your own CSS or if you wanted to change the content of a single page. The solution to this problem would be to create a meaningful class or id that targets that specific page’s elements, but you are still adding things, and this can be done whether or not you are using Bootstrap, hence why the Bootstrap library has really no concern over your overall layout in case you wanted to make small changes, and that is because you would just need to style a particular element with newer styles that would overwrite the existing Bootstrap styles. There are many solutions to your Separation of Concerns principle, one would be to use Javascript to change the styles accordingly, adding and removing classes from elements based on the url of the page, and there are many other ways.
I’m happy to help you if you have any questions regarding more in-depth subjects, and I hope you don’t take my answer the wrong way because I really don’t mean to discourage you in pursuing your ideas and research and talk about your knowledge; that is a great thing you’ve done today, know it.