A writhing mass of flesh, eyes, and tentacles ley like a mountain ahead. Tendrils of corruption and fear seep from the hulking body. This is the core of the Black Empire, the seat of N'Zoth's power, within the body of a god.
First, we know that N'Zoth is an incredibly large being - the Crucible of Storms was originally described as a "fragment of N'Zoth" in a Mamytwink interview from BlizzCon 2018. N'Zoth appears to be present underneath Stormsong Valley (near the originally speculated prison location from Chronicle) in Patch 8.1.5, but also imprisoned in Nazjatar in Patch 8.2 - a fair distance away. Perhaps a part of N'Zoth is imprisoned somewhere, but his full body is so much larger that it spreads beyond that location, like a vine that's grown beyond the supports that hold it.
Second, N'Zoth is also associated with corruption, ranging from the Emerald Nightmare to Neltharion the Earth-Warder, better known as Deathwing. Il'gynoth's whispers parallel several events in Patch 8.2, one of which referring to N'Zoth gaining strength: "From the earth, he draws strength. Our earth. Our strength." Instead of assuming that N'Zoth's prison was always underneath the Well of Eternity, perhaps N'Zoth was simply present, a small fragment that grew to reach the Well of Eternity and observe Azshara. We've seen Yogg-Saron extend his reach to corrupt the World Tree Vordrassil, so we shouldn't assume that N'Zoth's reach is also limited to his prison.