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It can't ignore the settings as far as I know. The git plugin (for better, or for worse) uses command line git to perform its operations by default. That means it is "stuck" with the behaviors of command line git.
If you'd like to try an alternate implementation, you can add "JGit" as a git implementation in the Jenkins global configuration. It is not as feature rich as command line git, but it covers many of the use cases very well, and does not rely on command output parsing.