You're thinking too much about this. My advice, go for the SDAC/OL-DAC + Atom, because the solid state amplifier is going to be the most neutral and/or transparent amplifier/combo at that price point.
You can always get tubes later. I honestly don't have direct experience with the Jot, but I do know that you absolutely do NOT need the 6 watts per channel that thing puts out for the 6XX. Also, the Jot is an older unit and I believe the consensus is that the Atom is one of the cleanest Amps you can buy right now.
It's very much up to you, and I'm sure some other guys who know more can chime in, but really, I think as of right now, you'd be best served by the Atom+SDAC/OL-DAC combo.