After all this time, did anyone find a solution? I had this problem in the past and thought it was specific to that user exit function group, but I'm having it now for a different one.
I suppose it's because of the way includes are structured, but there has to be a solution. As already exposed here, updating navigation index / restructuring object list does no good. It is annoying when syntax checking, because it hides the possible real errors that you only face when activating.