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.
That sounds suspicious to me, as well.
My understanding of the Fathom is that the passthrough is/should_be transparent. However, my ears tell me something's up.
You mean the Supernova's passthrough, right? Since you are going through the Supernova to get to the Fathom?
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.
Right - use a Y adapter at the output from the 1070 and go straight to both subs. That simplifies the equation a bit.