makeSetupHook broken in __structuredAttrs __bootPackages

[Artturin]

$ nix build --impure --expr "with import ./. { config = { structuredAttrsByDefault = true; }; }; stdenv.__bootPackages.stdenv.__bootPackages.stdenv.__bootPackages.stdenv.__bootPackages.stdenv.__bootPackages.stdenv.__bootPackages.libxcrypt"
this derivation will be built:
  /nix/store/994qfy50ylyafndz12zh8zq1a73gi5ll-libxcrypt-4.4.35.drv
building '/nix/store/994qfy50ylyafndz12zh8zq1a73gi5ll-libxcrypt-4.4.35.drv'...
libxcrypt> structuredAttrs is enabled
libxcrypt> unpacking sources
libxcrypt> unpacking source archive /nix/store/spzw99ag9wq184zd9il0n66937m30dzl-libxcrypt-4.4.35.tar.xz
libxcrypt> source root is libxcrypt-4.4.35
libxcrypt> setting SOURCE_DATE_EPOCH to timestamp 1686071870 of file libxcrypt-4.4.35/config.h.in
libxcrypt> patching sources
libxcrypt> updateAutotoolsGnuConfigScriptsPhase
libxcrypt> Updating Autotools / GNU config script to a newer upstream version: ./build-aux/m4-autogen/config.sub
libxcrypt> cp: cannot stat '@gnu_config@/config.sub': No such file or directory

broken hook can be found with

nix build --impure --expr "with import ./. { config = { structuredAttrsByDefault = true; }; }; stdenv.__bootPackages.stdenv.__bootPackages.stdenv.__bootPackages.stdenv.__bootPackages.stdenv.__bootPackages.stdenv.__bootPackages.updateAutotoolsGnuConfigScriptsHook"

Originally posted by @Artturin in #237968 (comment)

[Artturin]

ok good the issue is not actually that complicated since it happens in nix build --impure --expr "with import ./. { }; updateAutotoolsGnuConfigScriptsHook.overrideAttrs (_: { __structuredAttrs = true; })" too, so it's just a issue of substitutions not being in env attrset

[Artturin]

#240759