It’s already that way (at least on the ford site in USA).Maybe Ford should delete the roof rails on any Escape equipped with the sunroof. That would eliminate any confusion.
If you select a package that has a moonroof, then try to select the cross bars, it tells you that you can either keep the moonroof or remove the moonroof to add the cross bars.
If you add the cross bars first, and try to add the moonroof package, the same thing occurs.
if you mean getting rid of the mounting rails on some models, I think that would probably be a bigger engineering issue (and cost, now you’re making even more parts) but I’m not an engineer. It’s also possible they’re working on a future solution, that happens a lot with a full redesign.