but no mention of what to do with a 3-wire circuit
through conduit. Red, black, white
(and green) sounds like the reasonable thing to do,
but I want to make sure it doesn't violate
some obscure rule I'm missing...

I'm not a professional electrician, but I can tell you that most
subpanels I've seen are fed with two black wires for the two hots, and
that black and red is also a combination I've seen.

That said, your local inspector might not really care what the NEC
allows, he might insist that you have some arbitrary color scheme (and
he may even be able to pull the local codes out of his ass,err, um,
back pocket.)

Tim.