If multiple packages use this method (adding a class that adjusts left-padding and sets a left border), only one is able to show their line highlight.
@lunixbochs, could you link to the highlight method you are referring too? I can't find any referenced to a highlight method in the git-diff code.
I know what he means. I think the issue is really real estate. It's a lot less intrusive than the icons (which you can switch on).
If you have a specific use case and ideas for making it play nicer, let us know. For now, I'm going to close this as a wontfix.