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I thought of the same genes part as well but the rats were more than happy to eat me and hugo before he discovered he could control them.
Maybe the genes are latent?
The game was a "one-and-done narrative experience" according to the narrative designer.
https://gamingbolt.com/a-plague-tale-innocence-developers-have-no-plans-for-sequels-or-dlc
They are however are giving very vague hints at something upcoming. + SteamDB shows that there is some additional DLC happening.
Lucas tried the explain the phenomenon as follows "If only I knew... The Great Break... Its aftershocks continue to ripple through time... ".
The Great Break is supposed to be the time when the Macula leaves dormancy and manifests into the original state. In other words, it awakes, thus makes its carrier known to the outside world as so by having him or her displaying certain symptoms. Hugo already went through this state sometime after his birth, and years before the events of the game.
I think the rats have a certain connection with the Macula and can somehow sense it, along with anything that has a certain relationship with it or its carrier(Robert, the servants, Hugo's room), which I think is what Lucas means by "aftershocks", so they tend to leave them alone. Amicia was kept from seeing Hugo for years, which should make her an exception.
The elixir is meant to slow the progress of the Macula, forcing it to return to its original state so the carrier can have more time to prepare for the first threshold. The same applies so the rats tend to stop when it's done.
As for Hugo himself, the rats will still attack him by the time he starts to gain the Imperium ability, but not anymore when he later attacks the castle with Nicolas, he still hasn't passed the first threshold by then. So I think the carrier himself might need special training to let the rats sense the Macula in its living state, which should be taught by Vitalis and possibly along with Beatrice, Vitalis does somehow admit that during the final confrontation.
I think the Macula is supposed to be that mastermind. The rats tend to have a shared intelligence as you say, when the Macula somehow begins to take effect.
I think the game kind of explains them as such, but maybe not in a very clear way.
Reference:
https://aplaguetale.fandom.com/wiki/Prima_Macula
In "All That Remains", the rats initially tend to leave Robert alone but attack nonetheless when Amicia and Lucas arrive, maybe it's the scent of the living that encourages the rats to attack despite their fear for the Macula. The servants however, are not in their way of attacking so they continue to ignore them. Also they tend to converge and go towards Hugo's room, the Macula effect somehow lures them yet prevents them from getting in, they're already grouping in the room towards Beatrice's study when Amicia and Lucas finish with the searching, and they don't hesitate to regroup into rat swirls to attack.
The elixir however, has the link to the Macula that's so strong, strong enough to be able to calm down the entire rat horde. It's also noticeable that the rats tend to ignore Hugo's Imperium command if they're busy feeding.