pkgconfig sets parameters for eolian_gen which include -S parameters. But if the same variable is passed as parameters to eolian_cxx they fail because eolian_cxx doesn't understand -S parameter. Which it doesn't need to understand, but it shouldn't fail.
I think @xavi would have liked your explanatio in the commit message (as an updated patch) itself and not only here in the review system.
With these two changes I would be ok with the patch.
How about. "Will be ignored, only for eolian_gen compatibility"?