I also experience this annoying issue. Found this interesting precision on StackOverflow: https://stackoverflow.com/questions/68584885/how-does-xcode-decide-what-preprocessor-macros-and-other-build-settings-to-use-f
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I encountered the same issue (previously using both background and background-darkAqua) and just found out the solution: make sure each one of them reference a different image file. Like so:
<background file="background.png" mime-type="image/png" scaling="none" alignment="left"/>
<background-darkAqua file="background-dark.png" mime-type="image/png" scaling="none" alignment="left"/>
Hope that helps.