Using pre-commit.hooks with a python project causes PYTHONPATH to have default site-packages

[wkral-netlync]

Describe the bug
When one or more of the pre-commit.hooks are enabled while languages.python.enable = true; and languages.python.version is set to something different than the default version of python in nixpkgs the resulting shell will have a $PYTHONPATH with site-packages from the specific version created in the venv, and site-packages from the default version of python plus additional packages from other python libraries used by pre-commit.hooks.

The resulting shell can have multiple libraries conflicting with each other for me this manifests as cffi library:
Exception: Version mismatch: this is the 'cffi' package version 1.17.1, located in '/nix/store/bw9h2axgbrd7fs9zbz00dx5a9404xqqn-python3.12-cffi-1.17.1/lib/python3.12/site-packages/cffi/api.py'. When we import the top-level '_cffi_backend' extension module, we get version 1.15.1, located in '<redactect>/.venv/lib/python3.11/site-packages/_cffi_backend.cpython-311-x86_64-linux-gnu.so'. The two versions should be equal; check your installation.

To reproduce
Please provide an Short, Self Contained, Correct (Compilable), Example by creating a gist using devenv.nix, devenv.yaml, and optionally devenv.lock.

Make sure to include full logs and what you expected to happen.

devenv.nix

{ ... }:
{
  languages.python = {
    enable = true;
    version = "3.11.9";  # Default version: 3.12.7
  };
  pre-commit.hooks.isort.enable = true;
}

devenv.yaml

inputs:
  nixpkgs:
    url: github:cachix/devenv-nixpkgs/rolling
  nixpkgs-python:
    url: github:cachix/nixpkgs-python
    inputs:
      nixpkgs:
        follows: nixpkgs

$ echo $PYTHONPATH
/nix/store/pn115q790hg1z6a0g3q84zy084ls2w07-devenv-profile/lib/python3.11/site-packages:/nix/store/3nxyxd2p2d5kvmznsdgi0j2z6as3hbdw-pre-commit-4.0.1/lib/python3.12/site-packages:/nix/store/d7wly0zny9cwmqyx70jysyihd3zvw9ml-python3.12-cfgv-3.4.0/lib/python3.12/site-packages:/nix/store/zv1kaq7f1q20x62kbjv6pfjygw5jmwl6-python3-3.12.7/lib/python3.12/site-packages:/nix/store/zsj4l3sqq35fysmhhysj1xmi01bs1wqa-python3.12-identify-2.6.2/lib/python3.12/site-packages:/nix/store/bxaxs52882h8l5impq97sfndw3zaqqxm-python3.12-editdistance-s-1.0.0/lib/python3.12/site-packages:/nix/store/bw9h2axgbrd7fs9zbz00dx5a9404xqqn-python3.12-cffi-1.17.1/lib/python3.12/site-packages:/nix/store/4drm9zi486w2jcpsml70zkmsd8136ipm-python3.12-pycparser-2.22/lib/python3.12/site-packages:/nix/store/ziygfgrrfki93xcr567isy6j2431qp7i-python3.12-pytest-8.3.3/lib/python3.12/site-packages:/nix/store/px86rl62fxcvbm7hpciyizq0yq3bzhac-python3.12-iniconfig-2.0.0/lib/python3.12/site-packages:/nix/store/qnfndbdg0k5s7zb47l5q9h7cszi56gpf-python3.12-packaging-24.1/lib/python3.12/site-packages:/nix/store/cdg583c1xq8njwxjky1zj3qmix3hpl08-python3.12-pluggy-1.5.0/lib/python3.12/site-packages:/nix/store/gmkkyg2l4iq23vdbara7krnr2j08fy8m-python3.12-ukkonen-1.0.1/lib/python3.12/site-packages:/nix/store/nipgxfzw0wdk03h88dcbnwnw8wwkh8f7-python3.12-nodeenv-1.9.1/lib/python3.12/site-packages:/nix/store/j7q50pmxnawpif7kfimy51mjhjdjldns-python3.12-pyyaml-6.0.2/lib/python3.12/site-packages:/nix/store/d1r4w7mhq6v7vvr0r8cf3wi4jhmyrdik-python3.12-toml-0.10.2/lib/python3.12/site-packages:/nix/store/8xbcm89jwys1dzarwpbm37n0nwrsq1i7-python3.12-virtualenv-20.26.6/lib/python3.12/site-packages:/nix/store/d1q63libwiaylpjgs6cdi851myz42n6y-python3.12-distlib-0.3.8/lib/python3.12/site-packages:/nix/store/imyrdiwdg86f20sf4k5p7qp6cqch854i-python3.12-filelock-3.16.1/lib/python3.12/site-packages:/nix/store/1hci0iw7l2b54xgal7hk02a6va1b9sbm-python3.12-platformdirs-4.3.6/lib/python3.12/site-packages:/nix/store/fyfidwrpq0d5sz92x3vzly1249bkhsys-python3.12-isort-5.13.2/lib/python3.12/site-packages

Note that it doesn't have to be a python based hook, any will cause the issue from my testing.

devenv.nix

{ ... }:
{
  languages.python = {
    enable = true;
    version = "3.11.9";  # Default version: 3.12.7
  };
  #pre-commit.hooks.isort.enable = true;
}

$ echo $PYTHONPATH
/nix/store/k0499g0yp243rylwa12vrc8ysdjxbhlc-devenv-profile/lib/python3.11/site-packages

I expect with the pre-commit hook enabled that $PYTHONPATH would be the same as without it enabled and whatever dependencies are needed to run the hook would be isolated from the devshell.

Version

Paste the output of $ devenv version here or tell us if you're using flakes.

$ devenv version
devenv 1.3.1 (x86_64-linux)