For some reason, it complained about NRT, but not SYD.

Yes, that it a touchy one, and why I didn't originally pick that segment. But at least the calculator thinks it's legal.

The calculator also tells me on occasion that a 90 minute connection in MUC is illegal, and usually won't let me book SIN-NRT-SFO with a 40 minute connection on UA804/838. I don't put too much stock in it if I know what's realistic.

I would call the 1K desk, book the whole thing through them, and confirm that the MEL UA SYD UA SFO is legal, when not booked as MEL UA /X SYD UA SFO. I just don't trust the mileage calculator by itself on this type of thing. Just going to united.com (a slightly more reputable source), I cannot seem to book MEL-SYD-SFO with a stopover in SYD.

Until someone from United or the Australian authorities says otherwise, I think that the ability to book MEL-SYD-(USA) with a stopover in SYD is a bug in the mileage calculator that is a result of the need to incorporate transfers between the MEL-SYD-LAX flight and the SYD-SFO flight.

TG991/992 go BKK-SYD-BNE-BKK, and a year ago it was possible to book SYD-BNE by itself with either flight number. However, I believe it was Kiwi Flyer or DownUnderFlyer who advised against it. Now, TG991/992 are no longer listed as options for SYD-BNE.

Perfectly legal to have a stopover on UA if doing MEL-LAX via SYD provided the international segment is on UA.
UA's traffic restriction on SYD-MEL is "stopover or connecting online traffic only".
I doubt SIN-SYD-MEL would be allowed, despite the MEL part being a part of the international leg to LAX/SFO as the connecting flight onto that segment is not online.