Yes, it might break embedded features like comments unless you whitelist the allowed uses. I would assume Firefox handles this thoughtfully, but I haven’t tried the new cookie jars yet, so I don’t know what the UI looks like or allows.
Elsewhere they mentioned that there are exceptions for "popular" SSO systems, but I have a hard time imagining any exception that would allow a shared login for Facebook comments while blocking Facebook tracking across sites. These are essentially the same mechanism.