Ah Ha, you have spotted the flaw with the genuine Ford roof bars as the do not lock, and could be stolen.
Same problem was on the previous non-facelift model. So it seems they never sorted it out for the facelift model.
You may have to come up with some sort of locking method yourself, or cover the heads with epoxy glue to prevent removal (permanent), or use an anti-tamper screw head method DIY style. Or just live with it as is.
Some aftermarket roof bars (not genuine Ford, other manufacturer) do have locking plates with a key lock. Unfortunately a bit late advice for you though.