AFAICT #3 (JL1 SFO-HND) is aimed at business travelers like me going HND-SFO-HND.
Exit Haneda around 5am and enjoy the last N minutes to the office in a cab.

Supposedly you'll get a good night's rest on the flight unless you're someone like me who has trouble sleeping in any moving vehicle.

Note that JL 1 used to leave at 6:30pm and arrive at 10:30pm; I've done this one several times with mixed results. IMO that was worse for leisure travelers because you're scrambling to figure out how to get to your accommodations since the last train out of Haneda is quite soon after arrival (and a bunch of DL flights land around then too, adding to the queues).