`lint.per-file-ignores` option is ignored by native server in `ruff.toml`

Basically it's the same issue as https://github.com/astral-sh/ruff/issues/11751 but the problem still occurs when using `ruff.toml` as config file.

jic: this happens in VS Code, when `ruff check`ing via console everything's okay.