Because excluding an extra means “install this as if the extra were not specified”, surely this would be resolved exactly as it would be today, by including the packages from thing.
We discussed this a bit in The ‘extra’ environment marker and its operators, and while there was disagreement, it seems pretty clear that contradictory extras can exist and should be caught at resolution time (or later when things don’t work), and that these are a bug in the package, but it shouldn’t matter here.
As an aside, I regularly use/recommend pip-compile to get all the dependencies into a requirements file, then modify it manually and install with --no-deps to exclude dependencies. Would not be opposed to using an extra for more targeted handling, but it works fine.