lintCommand does not work with useFlatConfig

[MrEfrem]

Describe the bug

I use different ESLint config files:

1. For IDE with a standard name (eslint.config.mjs). It contains more warnings.
2. For CI, Vite Checher with disabled some rules.
   I set lintCommand to eslint -c eslint.config.ide.mjs ...
   With an old ESLint (below 9 version) Vite Checker use my different ESLint config and I don't see any excess warnings in a terminal or Vite Checker UI.
   But with the ESLint 9 when I use useFlatConfig flag lintCommand doesn't work.
   dev.overrideConfig doesn't work with useFlatConfig too.

Reproduction

Set useFlatConfig: true, lintCommand: "eslint -c eslint.config.ide.mjs ."

Expected behavior

When using useFlatConfig Vite Checker should process lintCommand and dev.overrideConfig.

System Info

System:
    OS: Linux 6.8 Ubuntu 24.04.1 LTS 24.04.1 LTS (Noble Numbat)
    CPU: (12) x64 Intel(R) Core(TM) i7-8700B CPU @ 3.20GHz
    Memory: 23.95 GB / 31.19 GB
    Container: Yes
    Shell: 5.2.21 - /bin/bash
  Binaries:
    Node: 18.20.2 - ~/.nvm/versions/node/v18.20.2/bin/node
    npm: 10.9.1 - ~/.nvm/versions/node/v18.20.2/bin/npm
  npmPackages:
    vite-plugin-checker: ^0.8.0 => 0.8.0

Additional context

No response

Validations

• Read the docs.
• Check that there isn't already an issue that reports the same bug to avoid creating a duplicate.