These photos are an interesting addition to the conversation; and we are still waiting confirmation about the radiating status of the 28R LS. I see PAPI's on LHS of rwy threshold; I see standard green threshold lights; I see standard approach light & touchdown zone lights. That looks like a runway. I can't believe taxiway C had anything like this, so how can you line up on a strip of concrete, at night, that you can't see too well anyway, that doesn't have appropriate lighting. That's all you can see at 4nm, not the concrete/tarmac. I'm also surprised they could see a/c lights hidden in all the airport lighting. They would have been 2 candle power compared to what was surrounding them. But they said they could see something odd.
What approach did they brief at TOD? It can't have been only some kind of visual; they must have briefed an IFR approach of some kind and set the nav boxes for it. If 28R ILS was in the air it should have been tuned and identified, surely? How far out were they when cleared for this odd, last minute offset visual? To an unfamiliar crew that would be a huge cheese hole, right there, if it's last minute and unbriefed. (A bit like ATC asking you to take the next exit just as you touch down. It's a bit late now, mate)
If 28ILS was in the air, and if it was tuned and displayed, what was PM looking at on finals? It would have shown almost full scale deviation at 4nm. What calls does AC have on their approaches? It does seem like 2 heads outside ands no-one managing in the office inside. Were they in autopilot CMD or manual? If A/P, was CMD what was it following; FMS, VOR or ILS? If manual were the FD's on and what were they following? It would seem that they should follow 275 until passing the bridge and intercepting 284, by what ever method laterally.
If they were lined up with the taxiway, which seems invisible in the photos, what were they using for glide path guidance?
One reason that dismissing this as a minor event is not a good idea, is that no-one will investigate and find out how the holes lined up. Damn sure it will happen again. Time to plug the holes.