I just tidied up a few things in the Introjucer. Now this "Upgrade to recommend settings" warning should not appear anymore when you re-save a project.
We’re aware of this and we’re currently in the middle of overhauling all of the exporters. When this is done some of the recommended settings problems will be fixed. Others require framework code changes and I think it’s best to address these once the new exporters have been released and tested properly.