Probably nothing to do with paperwork, but the fact that they have to dispatch a relief crew.

If the report from earlier in the thread is correct (family emergency for a crew member), then presumably that pilot turned around and deadheaded back home on the next flight. That puts them one crew member short for being able to fly SIN-SFO nonstop when that crew makes their normal turn (I’m guessing two days later), so three pilots instead of four. With those three pilots, they can make it as far as HNL, and UA then only needs to dispatch two pilots from the mainland to HNL, on a (relatively) short deadhead.

If they did the stop in NRT, then they’d need to dispatch three relief pilots to fly NRT-SFO, and those three pilots would need not only a longer deadhead to get to NRT, but probably longer on-ground rest time. There’s a good chance they wouldn’t be able to arrange that in enough time to avoid further delay on the NRT-SFO segment. So, stopping in HNL makes the most sense, both operationally (fewer pilots needed, easier to get them to HNL on a ton of flights, less rest needed) and financially (pay two pilots instead of three, and pay them for fewer hours). International paperwork doesn’t even need to enter into the equation.