It'd be difficult to make a stereo NES, simply because the mixing of the two pulse channels (square DAC's) happens inside the 2A03 chip, and put onto Pin 1. The TND pin, with triangle/noise/DMC channels, is mixed with that externally, so any stereo panning would require a third-party CPU ASIC, or modded panning hardware on the board.
The mod for split audio is talked about here: http://hackitup.tumblr.com/post/3039352465/hacking-the-nes-famicom-for-split-audio-outs
The problem is, it would be hard-panned, without any external expansion connections or I/O or "special logic".
The most ideal way to get expanded audio from an NES or Famicom would be to put the audio connector on the cart itself, much like expansion carts for some other systems (I believe the Sega 32x and CD does this, but I'm not 100% sure).
Putting it in Famitracker would be obtuse to the goal of making a chip-accurate chiptune synth; the stereo NSF's generated would need custom hardware, and FT seems to be focusing on the core 2a03 variants and released cart expansion chips.
Now, if you do want stereo panning, it's quite easy to export channel-by-channel, and operate on it in Audacity or another audio editor.
Keep the panning resolution 4-bit (16 levels, 0x7 center), though. I wouldn't see them putting 8 or higher on hardware of the day.
One feature worth considering to add to FT, though, is the ability to batch-export channel by channel, with or without bypassing the APU system's mixers.
[p.s. you could also use two NES's, i.e., make two Famitracker instances. Synchronizing them might be a pain - I put a time code (set of pips, think like BBC does) in triangle 7F on both patterns, and sync them up that way.]