I tried and the bass-treble and front-rear are intact. Now they are set to zero (neutral) except from front-rear which was set full front. Actually even my rear speakers are left in (they just were on zero level by the full front setting) and produce funny flat sound (the original one) if I adjust more to rear.
I don't see any functionality missing.
So the signal comes out from the OEM radio preamp towards 3Sixty2 - which was the goal (thats the signal that 3Sixty2 suppose to manage or "flatten").

But for the rear speakers i think the original wiring and connection have left remain.

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X5 3.0d - Space Grey , Beige Leather, Burl Walnut Trim, SatNav, Rear Camera, Sunroof, Light Package, 19" 212 Wheels, Tint, Power Fold-in Mirrors. AUDIO: Morel Elate 6 Audiophile Speaker System with Genesis Dual Mono Amp and Rockford Fosgate 3Sixty.2 DSP