We use different operating systems but our main systems use Windows. Therefore we have the Default Git directory under <jenkins_controller>/configureTools to be C:\blablabla.

In the normal agent configuration, this directory can be overridden but this feature is missing in the plugin when configuring a mac-cloud. 

Jenkins injects these paths after the environment variables or atleast ignores them. I put /usr/bin/git in the env-variable, but it still wants to use the C:\ path.

I would like to contribute myself but sadly I'm not good enough at developing plugins yet.

This probably has to interact with the git-client-plugin, which is responsible for said feature under ./configureTools.