A more succinct question would be "can antitrust laws override the ToS?" The answer is "yes". The FTC can even make Apple change its ToS through a consent decree (and possibly through other mechanisms as well). A ToS can't shield you from antitrust enforcement. In this case, it might even hurt Apple, especially if it can be shown that Apple doesn't consistently apply this rule.

But let's say it's not antitrust, which is what your question is trying to imply. Apple will still need to answer to the other ways it makes third-party messaging apps worse on iOS - automatic offloading and share extensions being two examples.