It'd be much better if Introjucer were to write the settings for the IDE projects to a "Introjucer.props" file (for Visual Studio) and "Introjucer.xcconfig" file (for Xcode) rather than messing with the project files themselves.
It'd be much easier to maintain and to override at the user discretion where needed.
Basically, using "props" and "xcconfig" files is like using #includes, but for project settings. It has saved me tons of hours.
You can put all sort of customizations in there and reuse them in multiple projects by simply reusing the same configuration file.
And on top of that, both IDEs let you override some of those customizations where you need to.