I'm putting the final touches on SetupHelper v8 beta. This version allows multiple packages to modify the same files using the unix patch utility. Packages must be written to patch rather than replace files it intends to modify.
GuiMods also has a test branch with some files switched to using patch.
I'm hoping some of you will help with the final testing. Please post here or best yet in the SetupHelper GitHub repo issues section with your comments and especially bugs.