[Bug] Set `shamefullyHoist` by `.pnpmfile.js` not working

[Airkro]

Verify latest release

• [x] I verified that the issue exists in the latest pnpm release

pnpm version

v10.24.0

Which area(s) of pnpm are affected? (leave empty if unsure)

No response

Link to the code that reproduces this issue or a replay of the bug

No response

Reproduction steps

// .pnpmfile.cjs
module.exports = {
  hooks: {
    updateConfig(config) {
      return Object.assign(config, {
        shamefullyHoist: true,
      });
    }
  }
};

Describe the Bug

shamefullyHoist: true not work when it config by .pnpmfile.cjs

Expected Behavior

shamefullyHoist: true should work.

Which Node.js version are you using?

24.0.0

Which operating systems have you used?

• [ ] macOS
• [x] Windows
• [ ] Linux

If your OS is a Linux based, which one it is? (Include the version if relevant)

No response