Scheduled journey times from NRT to SFO are typically two hours shorter than the scheduled times for SFO to NRT.

I'd always assumed this difference was built into the schedule due to the prevailing winds.

But perhaps it's actually because the airlines built in a 2.5 hour cushion for departures from SFO to compensate for delays there?. (and a 0.5 hour delay on the NRT side)....

Nah. I don't think so.