It doesn't have to be a weaker stack per se. It is also a lot about knowledge. WhatsApp vested much time into understanding FreeBSD. It may be if you vested the equal amount of time on Linux with knowledgable people, then you would see roughly the same performance.

If I should take a guess, the advantage of the FreeBSD stack is that it is simpler and easier to understand. Hence, it is easier to tune for performance.