Maybe those thoughts are indirectly survival-related? If an animal doesn't consider its own self and its kin/species to be of supreme importance, it won't effectively and wholeheartedly do the things needed to find food and escape predators and raise young (or the modern human versions). So in the face of all evidence to the contrary, we humans think we're hot stuff.
Regarding not being able to analyze a system from within a system, yes, I've wondered the same things as you about what our brains can and cannot process, no matter what tools we create to extend our senses. The 'universal' applicability of math does, it seems to me, come into question here. As does our use of language, which, when you look into that issue, can really make your head spin.
Head spinning, though, can be a good thing. The line of thinking you're exploring in this thread has actually contributed to my life happiness, and it continues to be of practical use. I'm interested to see where it takes you.