When this module was first introduced, it processed the runtime option
in a way that nested the resulting files and directories under an etc
directory.
https://github.com/NixOS/nixpkgs/pull/98506/files#diff-685092dbb1852fbf30857fe3505d25dc471dc79d0f31c466523b5f5822b68127R11-R21
That implementation relied on nixos/modules/system/etc/make-etc.sh, a
script that was later removed.
eb7120dc79
The implementation was updated to use linkFarm, which changed the
behavior slightly, in that the configured files and directories are no
longer automatically nested under an etc directory.
307b1253a7
But the module still configures neovim's runtimepath in a way that
assumes the old nesting behavior.
04f574a1c0/nixos/modules/programs/neovim.nix (L173)
Restore the original behavior, nesting runtime files and directories
under an etc directory.
418fda2293