An easy-to-imagine scenario is: a program which solves every NP problem we give it in P time, but we don't understand how or why it works. With bounded probability of error, this would constitute a proof of P=NP. But the program might elude human understanding.
Babai's graph isomorphism in quasi-polynomial time proof is approaching this. The algorithm involves handling one special case specially, so it's still within reach of human understanding. But you could imagine an algorithm that handled 1000, or a billion special cases specially, that would be beyond human understanding.
Babai's algorithm is constructed by a human, so there is an intuition behind it. But if such an algorithm arose through genetic programming, I can imagine not ever being able to understand it.
It's possible that factoring is similar: there exists an algorithm for factoring efficiently that involves a large number of special cases. Already, the best algorithms are damn complicated. If the minimum necessary algorithm is large enough, it might forever elude human comprehension.