python: fix venv creation; resolve sys.prefix to realpath

[qbisi]

An attempt tring to fix python's sys.prefix not targetting the realpath in python-env or python-venv . See #442540

Before

> nix-build -I nixpkgs=$HOME/nixpkgs -E '{pkgs ? import <nixpkgs> {}}: pkgs.python3.withPackages (ps: [])' -o result
> result/bin/python3 -c 'import sys; print(sys.base_prefix); print(sys.prefix)'
/home/qbisi/nixpkgs/result
/home/qbisi/nixpkgs/result

> result/bin/python3 -m venv --system-site-packages result-venv 
> result-venv/bin/python3 -c 'import sys; print(sys.base_prefix); print(sys.prefix)'
/home/qbisi/nixpkgs/result
/home/qbisi/nixpkgs/result-venv
> ls -al result-venv/bin/python3
/home/qbisi/nixpkgs/result/bin/python3

After

> nix-build -I nixpkgs=$HOME/nixpkgs -E '{pkgs ? import <nixpkgs> {}}: pkgs.python3.withPackages (ps: [])' -o result
> result/bin/python3 -c 'import sys; print(sys.base_prefix); print(sys.prefix)'
/nix/store/82hqqjwsg9xgm0mxmbj495hk6sfwd0iv-python3-3.13.7-env
/nix/store/82hqqjwsg9xgm0mxmbj495hk6sfwd0iv-python3-3.13.7-env

> result/bin/python3 -m venv --system-site-packages result-venv 
> result-venv/bin/python3 -c 'import sys; print(sys.base_prefix); print(sys.prefix)'
/nix/store/82hqqjwsg9xgm0mxmbj495hk6sfwd0iv-python3-3.13.7-env
/home/qbisi/nixpkgs/result-venv
> ls -al result-venv/bin/python3
/nix/store/82hqqjwsg9xgm0mxmbj495hk6sfwd0iv-python3-3.13.7-env/bin/python3

Things done

• Built on platform:
  • x86_64-linux
  • aarch64-linux
  • x86_64-darwin
  • aarch64-darwin
• Tested, as applicable:
  • NixOS tests in nixos/tests.
  • Package tests at passthru.tests.
  • Tests in lib/tests or pkgs/test for functions and "core" functionality.
• Ran nixpkgs-review on this PR. See nixpkgs-review usage.
• Tested basic functionality of all binary files, usually in ./result/bin/.
• Nixpkgs Release Notes
  • Package update: when the change is major or breaking.
• NixOS Release Notes
  • Module addition: when adding a new NixOS module.
  • Module update: when the change is significant.
• Fits CONTRIBUTING.md, pkgs/README.md, maintainers/README.md and other READMEs.

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