I'll try to get some clips of the two of them pushing some filters so you can hear the resulting difference. The two different outputs definitely react differently to different effects downstream. The "synth mod" sounds way better through the Zoom, in my opinion. Turns the Zoom from a mediocre gated synth fuzz to an excellent one, it never sounds that solid pushed by the normal OC-2 signal.
You can hear the EHX Muff'n fatten up the low end of the "synth mod" signal. But the "synth mod" doesn't push filters as well, I think too much of the signal is in the upper range VS the heavily focused low push of the normal OC-2. At least that's my theory. But I certainly am just guessing. I'll let the clips do the talking.