Gonk - one thing I didn't mention was that when testing the Fathom as slaved, even with the volume all the way up, it wasn't "THAT" loud - loud but not overpowering, and overpowering is what I would've expected with the volume maxed out on the sub (and the 1070's channel calibration set to 0.) This was part of what set off a red flag to me, that the Fathom might not be getting a good signal.

My understanding of the Fathom is that the passthrough is/should_be transparent. However, my ears tell me something's up.

So with your suggestion, I could Y adapt right at the receiver, send one cable to the supernova and another to the JL. I'd use another Y at the supernova per the manufacturer recommendation. I like it. I think that's what I'll try.
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Model 1070
Toshiba HD-A35 & Pioneer BDP-51
Tivo Series 3
Elite 50" / Aquos 32"
Squeezebox Radio

Stereo Setup:
NAD C326BEE (50Wx2)
Elite DV-47Ai Universal SACD/DVD-A
Citypulse DA7.2x II + TXCO DAC
B&W 685s
JL Fathom F112
Denon AH-D2000 Headphones