All programming languages/frameworks/libraries are abstractions. In order to use HTML, you don't have to learn how operating systems translate that into machine code instructions. Bootstrap is just an abstraction of CSS and JS.
Do you need to know CSS to do a few little things with Bootstrap? No. Would it be bad if you only learned Bootstrap and never learned CSS? Of course. Is that what FCC is doing? No. Is it going to hurt if your curiosity leads you to learn some CSS ahead of schedule? No. It might even be a good thing. But some people can only learn a few things at a time.
It's like if you wanted to become a harmonica playing, juggling, unicyclist. Some people would just want to jump up and start working on all three at the same time. Most would probably want to work on each separately and then start incorporating then together.
It's difficult to craft a learning program to fit all needs. People learn differently, at different speeds, get hung up on different things that may be obvious to others. If you want to look ahead at CSS, go ahead.
And I'm concerned about your word "master". If you wait until you master any of these, this is going to take years. In the course of this program, you are going to have to learn a dozen languages/frameworks/libraries. You probably aren't going to master any of them. Even professional coders haven't "mastered" may of these. They simply know them well enough that they can look something up when they need. But these technologies are too interrelated to learn them just one at a time.