As far as I remember, NixOS the operating system was a separate repo, but it lagged behind Nixpkgs the package collection.
Before the creation of overlays and flakes, it was a hard thing to sync them.
Now that they live in the same monorepo, it is way easier to update both a Nix package and its corresponding NixOS module.
Also it is way easier to make integration tests for each of them.
A long time ago I was talking with Okada about splitting NixOS into its own repo, but we never tried to do it.
Nonetheless I still advocate for a monorepo. Filling three PRs for a single package is annoying enough.
Further, NixOS is less than 8% of Nixpkgs monorepo, and the whole HM (plus dotgit) occupies just two NixOSes.
This particular problem will not disappear, since we do not have titanic barriers to include software.
Also, I have vented my complaint with multirepos a short time ago:
Hey, are you stealing my idea? Nops, I steal that idea before