What is it that you prefer about the Atlantis over the Pagoda? My top priority is bass control, midrange realism, and soundstage in that order. My trafomatic had soundstage to spare.
In short, I'm very treble sensitive and I love mids and bass. With the same tube, the Pagoda is brighter with a deeper soundstage. The Atlantis has good width, but not as much depth with the same tube as the Pagoda. It's a more mid-focused DAC than the Pagoda. The Atlantis also responds pretty dramatically (in DAC terms, anyway) to tube rolling, while the Pagoda signature gets tweaked a little less by a tubes. The Pagoda is a little more dynamic overall.
I like that the Atlantis responds so well to tubes and has 2dB rolled-off treble at 20kHz (vs. 1dB for the Pagoda). The Bendix can give you significant detail and clarity with a helping of treble, bass extension, and a slightly dryer signature. The GE Triple Mica tubes give you a good helping off bass and a lovely euphonic signature.
If you want added treble, nice bass extension, and insane soundstage, you can use 6N2P tubes with an adapter (I sent one to both @Soundsgoodtome and @Torq for them to try out). I still have a bunch of those tubes from Ukraine and several more adapters on the way from China. The treble gets a little more pronounced than I prefer with them, but I'm particularly treble-sensitive.
Really, I think no matter what you do, you'll be getting a lovely sound from any current MHDT Labs R/2R Tube DAC. All of them have amazing timbre and instrument reproduction, and all of them can be adjusted to taste with tubes. I think I've purchased 15-16 completely different tube types at this point to try, which is how I landed on the GE tubes (more bass, not more treble but still good detail, and a very tube-like sound). I almost stopped after listening to Western Electrics because they do great things for the soundstage and bass, but they also feel a little softer to me than the GE.
Soundsgoodtome posted some impressions here:
http://www.head-fi.org/t/798259/mhdt-labs-r-2r-nos-tube-dacs/75#post_12403552
As did I:
http://www.head-fi.org/t/798259/mhdt-labs-r-2r-nos-tube-dacs/75#post_12405385