Yes I followed the docs, and it doesn't work because fetchYarnDeps only supports yarn v1 (they have # yarn lockfile v1 as first line, which yarn berry doesn't have)

Funny enough, going the nodePackages at least allows me to build and run the package correctly, but it breaks the pipeline because generate script pulls in python2 for some reason

Hmm, the actual fetcher seems to work fine manually for me.
e.g. this works correctly:

{
  stdenv,
  fetchFromGitHub,
  yarn-berry_3,
  nodejs,
}:

stdenv.mkDerivation (finalAttrs: {
  pname = "verdaccio";
  version = "6.1.2";

  src = fetchFromGitHub {
    owner = "verdaccio";
    repo = "verdaccio";
    rev = "v${finalAttrs.version}";
    hash = "sha256-EssvN5HtGI5Hmw4EXetj5nzrkBZAAJGgOx09dlYJzhI=";
  };

  nativeBuildInputs = [
    yarn-berry_3.yarnBerryConfigHook
    yarn-berry_3
    nodejs
  ];

  offlineCache = yarn-berry_3.fetchYarnBerryDeps {
    inherit (finalAttrs) src;
    hash = "sha256-jzkmDxQtIFMa1LIPcvKKsXIItPntgXTavoWhd5eZWyQ=";
  };

  buildPhase = ''
    yarn build
  '';

  installPhase = ''
    mkdir -p $out
    cp -r build $out
  '';
})

Yes the fetcher seems to work

Try this

{
  lib,
  stdenv,
  nodejs,
  fetchFromGitHub,
  yarn-berry_3,
}:
let
  yarn-berry = yarn-berry_3;
in

stdenv.mkDerivation (finalAttrs: rec {
  pname = "verdaccio";
  version = "6.1.2";

  src = fetchFromGitHub {
    owner = "verdaccio";
    repo = pname;
    rev = "v${version}";
    hash = "sha256-EssvN5HtGI5Hmw4EXetj5nzrkBZAAJGgOx09dlYJzhI=";
  };

  nativeBuildInputs = [
    nodejs
    yarn-berry
    yarn-berry.yarnBerryConfigHook
  ];

  offlineCache = yarn-berry.fetchYarnBerryDeps {
    inherit (finalAttrs) src;
    hash = "sha256-jzkmDxQtIFMa1LIPcvKKsXIItPntgXTavoWhd5eZWyQ=";
  };

  buildPhase = ''
    runHook preBuild
    yarn run build
    runHook postBuild
  '';

  installPhase = ''
    runHook preInstall

    mkdir -p $out

    cp -r {bin,build,package.json,.pnp.cjs} $out/

    runHook postInstall
  '';

  meta = with lib; {
    description = "A simple, zero-config-required local private npm registry";
    longDescription = ''
      Verdaccio is a simple, zero-config-required local private npm registry. No need for an entire database just to get started! Verdaccio comes out of the box with its own tiny database, and the ability to proxy other registries (eg. npmjs.org), caching the downloaded modules along the way. For those looking to extend their storage capabilities, Verdaccio supports various community-made plugins to hook into services such as Amazon's s3, Google Cloud Storage or create your own plugin.
    '';
    homepage = "https://verdaccio.org";
    license = licenses.mit;
  };
})