Since you've stated you would really like to keep app-specific coding isolated in the app-specific macro group this may not be your ideal solution, but nonetheless, I think it may be your best practical one: instead of using If-Then-Else, you could use the Switch/Case action to create exactly the conflict controller behavior you describe for macros in a global macro group, albeit on a per-macro basis (though if you do this a lot, you could also use @DanThomas's KMFAM to create a reusable template pre-filled with the same apps to make it easier):
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