TRACON Controller reported misidentifying an aircraft's location resulting in issuing a descent below the MVA. When the issue was identified the aircraft was already entering an area that was safe for their altitude.

Narrative

We were initially on a Runway 27 op at SAN. Due to a few missed approaches we changed to a RWY 9/27 operation. This resulted in several aircraft to go into holding who had limited time to hold before they had to divert. We built in a chunk of time for Tower to get RWY 27 departures while the arrivals waited their turn to land on RWY 9. There were multiple people coordinating with me including the pilots asking about an ETA. Aircraft X was a previous go-around (they were on final to RWY 9 behind a Aircraft Y and told to reduce to final approach speed for compression; they only reduced their speed by 10 kts over 5 miles and Tower had to send them around) so I was eager to get them in to avoid a divert. While Aircraft X and the other RWY 9 arrivals behind them were westbound over the PGY VOR; the RWY 27 departures were climbing out on the ZZOOO SID which goes westbound; then south and east; opposite direction of my arrivals. My departures were not climbing as fast as I would have liked so I intended to descend my arrivals to the MVA ASAP. I normally use the PGY VOR as my quick reference when I can descend from 5000 to the next MVA. I made a quick glance and thought I saw the PGY VOR but I believe I actually looked at the Otay drop zone and descended my Aircraft X to 4000. They descended below the MVA. A coworker shouted across the room that Aircraft X was below the MVA and by the time I noticed what was wrong they were 1/2 mile or less from the edge of the MVA (going into a 3800 MVA) and I opted to not issue a low altitude alert because I thought it would add confusion on the pilots end since they were doing exactly what I told them. Recommendation - This is a complex and uncommon configuration that we run here. I would say most of my coworkers outside of the fairly senior ones are pretty uncomfortable running a 9/27 operation; but that's just my guess. It involves a bunch of coordination as to who is last arrival/first departure and vice versa as we are alternating opposite direction. I should have better utilized my MVA map instead of relying on my own visual aid; as that is clearly not a perfect solution.