I don't think these extra-galactic infrastructure would be reachable by human hacking.
Not directly by the humans, but the AI stuff in one galaxy talks to the AI stuff in the other. Corrupting the local copies is only part of what's going on.
I wouldn't find any simple explanation sufficient enough to overcome my expectations of a distributed, multiply-redundant network.
That's
okay, it's a game. Explaining the necessary loopholes about how the AI works, how it chooses designs, etc. limits our imagination on how its could conceivably work.
= = =
I would also find the Mark. V unlocks question interesting. Should players be allowed the tactic of disabling both standard I-IV fleetships and the core defending ships? Corruption to be more valuable in this respect (and might use it), and arguably where it
matters.
(BTW, even us diploid organisms seem to be capable of cross referencing intact copies in some forms of DNA repair. There's technically 4 copies of the same information, which allows the machinery to correct any single error.)