They probably got stuck in several cycles of that before the contrary evidence was overwhelming enough to break them out of their off-by-one mental model.
On approach you should be looking at the threshold and the numbers. That's right around where the X was, so it would be clearly visible to anyone trying to land on the closed runway. They were not trying to land on that one, and since they were over the taxiway the X was actually two "lanes" away from where they were. I don't think the X is terribly relevant to what happened here.
What we need is better computer guidance. The tech is available, our legislature is not. Look at the incredible "taking out freedoms" pushback against adsb to see what I'm talking about.
Also, due to the common airport design of runways and parallel taxiways, it isn't uncommon to fly either near or over waiting planes on final approach, so this may not have been cause for alarm even if they were equipped with ADS-B In.
Anyway, score one (more) for the robots, who would have picked up the correct ILS localizer.
In the words of the investigation: "At 2346:30 PDT, Northern California TRACON cleared ACA759 for the FMS bridge visual runway 28R approach."