I'll bite. Which is safer?

Yes, BART parking isn't perfect, but the stations on the peninsular are significantly better than others in the system. SFO airport parking also isn't without it's issue - there's been numerous reports of vehicles being stolen, broken into, wheels stolen, caught on fire, etc.

My car has spent collectively months of nights at Millbrae/San Bruno BART stations as airport parking, and I've never had any problems. Of course that's just one datapoint so hardly meaningful - but at a saving of >80% that's a fairly significant amount of money saved!