I would think it was much more likely that they couldn't directly see the light because the cliffs above them at their 200 foot flight level cut off the beam. I note that the aircraft would have been presenting a port side nav light towards the lighthouse. Is it possible that the aircraft navigation lights and anti collision beacon reflecting against low clouds could potentially mask the lighthouse red and white lights? I am making the assumption that they would be illuminated flying at low level on an intended approach.
Rereading the report, it looks like the crew didn't look at the page two notes of the approach pattern and were completely unaware that they were below MSA approaching Black Rock. That document and the way the route was presented is absolutely damning as the initiator of all that followed.
Many thanks to the contributors over the last few pages for your insightful and thought provoking posts. Much appreciated.