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.
The Spelljammer setting, which is where the Nautiloids and Illithid Empire lore crossover into Faerun from, the multiverse is absolutely massive. Toril is just 1 of like 9 inhabited planets in its own solar system, with one of those being an entire artificial planet serving exclusively as an Illithid forward base in Realmspace. There are potentially even more inhabited planets across all of the FR universe outside its solar system, and as many in all the parallel universes of the other settings like Eberron and Greyhawk, and there are hypothesized to be an infinity of such universes. And on top of that, add all the Illithid forces who are roaming around the endless Astral Sea.
So yes, they are quite precious and rare, but Spelljammer's definition of 'rare' is something altogether different than the quaint little bubble of FR. If there are only 4 docked Nautiloids across all the continent of Faerun that adventurers can find while still on Toril's Prime, that would be a few grain of sands in the grander multiverse. Granted, I don't know if Larian adopted the canonical Spelljammer scope when they added Nautiloids to their campaign, many campaigns don't because it's too vast to handle or rarely comes into effect.
Also, when Balduran is captured by the mind-flayer colony, he is seen held in some underground chamber surrounded by Illithids. However, when he is dominated by the Elder Brain, he is floating around with a bunch of other Illithids who are all spaced pretty far from each other and gazing up at the Elder Brain against a background of the Astral Sea. Which means it's either a mental image of their connection, although when Tav gets that mental representation it's usually a giant illithid face or a much more unrealistic environment, or the brain also maintains a presence in the Astral Sea where Nautiloids might be cruising around, since Illithid colonies are essentially just outposts in Spelljammer.
Lastly though, it would be virtually impossible for the Absolute to dominate every other elder brain in the multiverse, since its influence only barely extends to Baldur's Gate and its environs as it is. Maybe if there was some innate connection between all Elder Brains which allowed it to corrupt the whole system instantly, but their telepathy and psionic connection doesn't extend nearly that far, certainly not between planes and universes, which are much stronger barriers against all arcane and psionic abilities than a trillion Orpheus's would be able to muster.
It could've already swayed or even dominated some other Elder Brains to its cause, that I don't know. Hard to imagine it being every single one in the multiverse though, otherwise what was happening in Baldur's Gate should've been at minimum happening across all of Toril.
