If the winds and runway conditions (wet/dry) permit, SFO usually stays on 28L and 28R for arrivals, and 01L for 01R for departures. Looking back at today's METARs for SFO, I see nothing that would have forced them off this configuration.
OAK and SJC do indeed usually slave to whatever SFO is on, i.e. 29 at OAK and 30L at SJC, but there can be exceptions. I don't what time NWA129 got into SJC, or where from, but SJC's weather was much better than SFO and OAK, so my guess is that it was just more expedious for ATC/the flight at that moment in time to use 12R.
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