It would be implausible to believe that someone would set a waypoint a the point of diaster. (I remember from my younger days, When skiing through trees in powder, always look between the trees or you're sure to end-up hitting one.)

The autopilot (if it was set) must have been on "compass" or "apparent wind" mode. Othewise the route would have been set-up to go inside, outside, or (with a lot of care) through the Coronado Islands.

Those islands are unlighted, look very sailboat unfriendly, and have a lot of fishing activity in their vicinity (the Google Earth image of the South Coronado Island shows nets clearly).

Seting a "Route" which was safe would in this case have avoided big problems.

http://members.marinasailing.com/ShowYacht.asp?YachtName=Aegean [previously listed in a thread below]

I note from the pictures of the boat that the chart plotter and instrument clusters appear are at the helm of the Aegian -- but there was little at the nav station.

It's GOOD to have these at the helm (where the watch crew is); however, there appears to be nothing below. Maybe they were running with a laptop which would have provided audio alarms below?

Anyway, as Jon postulated -- if the helmsperson was not there anymore (or asleep, or whatever) AND there was only one person topsides to start with, then Que Sera, Sera.