As you say, REF isn't meant to give an overall ranking in that sense, and there is no real way to combine results across all subjects in a manner which makes obvious sense.
Also, remember that different universities had different REF strategies - some chose to optimise their (average) GPA by only submitting staff who were going to do well, while some chose to optimise their 'research power' (quality*quantity) by submitting more people. The somewhat silly staff exemption rules in REF give universities quite a bit of flexibility when it comes to artificially increasing/decreasing their score, depending on whether they value a high ranking (quality only) vs more funding (quality*quantity)
It just doesnt make any sense to amalgamate the rankings together like that, but obviously the media is going to do it since it generates click bait.