I think the netherbrain already dominates other elder brains in the multiverse. Where else would all these nautiloids come from in the end ? Certainly not from the colony under moonrise towers. And Omeluum said the knowledge to build them was lost, so these must be very old, precious artefacts coming from wide and far and not easily turned over by their owner brains..... Although the easy answer would be, another inconsistency in Larian's storybook.
There's a tablet on the Nautiloid at the beginning of the game that contains the schematics of the nautiloids. The design may have been lost, but it certainly isn't now. Omeluum is just not up to speed with what the Netherbrain knows.
