I would never burden a new construction home with a J-box in a basement that someday may become a problem for someone wanting to finish the basement.
I would set a 2 Gang adjustable box half inch off of the joist, facing down, so that if sheetrock were ever added, all they would have is a cover plate in the ceiling. No need to move electrical or bury a junction box. And I would go with the adjustable just in case they add furring strips and the drywall is an inch or inch and a quarter down from the floor joist. I would also run the wire up in the joist and drill where necessary so that a ceiling could be added later on without moving wiring.
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As mentioned, pulling two 12 / 2 NM cables at once is simply a matter of having two rolls on hand, or pulling a length off of one roll, taping it to the roll then pulling two cables at once off of 1 250 (or 100) foot piece.
A multiwire branch circuit will have less voltage drop than two 12/2 cables. The 12 / 2 / 2 saves a little bit of time in that you only have to deal with one ground wire, you wouldn't have to rig two cables, and you don't have to worry about share neutrals or 2 Pole Breakers or handle ties.
Eta: if the homeowner is thinking about adding things in the future, and the panel will be hard to get to, do yourself a huge favor and run an extra 12 / 3 and 14 / 3 to the basement and to the Attic. That will give you 8 potential extra circuits in the future with wire that you probably would have thrown away anyway. If they even have once mention the word Spa, go ahead and run a piece of 1 inch ENT to the basement