I think Ford is using any damn excuse they can to deny warranty claims, they are now thinking like an insurance company, take your money and then deny as many claims as they can. Too bad they have not come to the realization that they are NOT an insurance company and the vast majority of their income comes from the sale of new vehicles. These petty refusals are costing them 10's, possibly 100's of millions in new vehicle sales.
I had the positive terminal on my factory original Ford battery fail. It leaked and took out the positive battery cable terminal. We all now know that Ford will not replace just the terminal on the battery cable even though it is available as a separate part, they mandate replacement of the entire power harness which is about $600 to $800 P&L depending who you ask.
In my case they denied all the warranty work (battery and harness) because they said the battery is not a warranty item. OK I know battery is not a warranty item, but their excuse is (like OP) a non warranty item (like battery or brake pads) takes out a warranty item and they get to not cover the clearly covered warranty item - that is complete and total bulls**t. The next thing we are going to be hearing is "yeah" you have Ford Motorcraft pads, but a Ford dealer did not install them, so we won't cover the caliper replacement.