With this flake:

{
  inputs = {
    nixpkgs.url = "github:nixos/nixpkgs/nixos-unstable";
    flake-utils.url = "github:numtide/flake-utils";
  };

  outputs = {
    self,
    nixpkgs,
    flake-utils,
    ...
  }:
    flake-utils.lib.eachDefaultSystem
    (
      system: let
        pkgs = import nixpkgs {
          inherit system;
          overlays = [
            (final: prev: {
              duckdb = prev.duckdb.overrideDerivation(old: {
                cmakeFlags = old.cmakeFlags ++ ["-DSKIP_EXTENSIONS=jemalloc"];
              });
            })
          ];
        };
        python = pkgs.python311;
        buildInputs = with pkgs; [
          (python.withPackages (ps:
            with ps; [
              duckdb
            ]))
          duckdb

        ];
      in
        with pkgs; {
          devShells.default = mkShell {
            inherit buildInputs;
          };
        }
    );
}

I can successfully build duckdb without jemalloc, but the python package (python3Packages.duckdb) is still using the version of duckdb from before the overlay. To test:

echo "SELECT installed FROM duckdb_extensions() WHERE extension_name='jemalloc';" | duckdb

Returns false, whereas:

import duckdb
assert not duckdb.connect().execute("SELECT installed FROM duckdb_extensions() WHERE extension_name='jemalloc';").fetchone()[0]

Fails.

Clearly, I don’t know how to override the input to python3Packages.duckdb. I thought that setting an overlay would propagate across the whole of pkgs (in the let bind) so that pkgs.python311.duckdb would end up being passed the overlayed duckdb.

How ought I to go about this? And what have I got wrong about overlays?