If the current model - merger of multiple prokaryotes - is correct, then the linked article (which says "And in more than 3 billion years of existence, it happened exactly once.") is incorrect. Nuclei, mitochondria, and cholorplasts represent 3 distinct merger events here on Earth. Actually, the article even mentions nuclei, mitochondria, and chloroplasts all being likely endosymbionts, then goes and repeats the claim of uniqueness.

In any case, if it can happen 3 times on one planet, it probably isn't dramatically unlikely, especially since at least one of those three events (chloroplasts) is strictly unnecessary for intelligence (in that no known intelligent species possesses them).