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I'm somewhat fanatical about backward compatibility, and removing "Clean after checkout" (or mutating it to be "Clean before checkout") would risk all sorts of compatibility problems. The git plugin (and the git client plugin) are two of the most used Jenkins plugins. Many users depend on them to remain compatible from one version to the next, and to retain their old behavior (no matter how odd that behavior may appear).
I'm glad the "git clean -fdx" was sufficient, since that retains compatibility with the existing code and existing job definitions.