So a here are a few example of where this would useful in developing cross platform games.
-Using third party plugins i.e. Like FGL which brings up a debug menu whenever the game starts. I could disable the plugin and so have just one capx that works with multiple platforms.
-Using plugins that aren't supported by Scirra Arcade. I believe that if any plugins are used that aren't supported you cannot submit to it. Again if you building a game for multiple platforms you will more than likely use additional plugins to provide services. So if you could disable the extra plugins you wouldnt need to again make a copy of the capx and strip it down.
Essentially what I am trying to avoid is branching when supporting multiple platforms, as it means one game change has to be replicated X times. If there are ways around this that I don't know about then please let me know.