Hi O. When you said, "An interesting conundrum. If we accept the B1200D idea we sacrifice the built in two channel mixer to use the sub."
Here's what I do. I don't know if it addresses the concerns you noted, but here goes...
On the S1 Pro, I use channel 1 for vocals and channel 2 for guitar.
I'm not interested in the subwoofer feature on my vocals. So I connect my mic straight to channel 1 on the S1 Pro and avoid the subwoofer all together. I adjust the EQ for the vocals/mic via the S1 Pro's mid and trem controls.
For channel 2 (my guitar channel), I want a deeper and more present bass sound. This is where the Behringer B1200D Pro subwoofer comes into play. (BTW, I use a Boss OC-3 Octave to get this lower bass sound.)
I input my guitar first into a channel on the subwoofer and then output it from the subwoofer to channel 2 on my S1 Pro. I use the Behringer's high cut feature to minimize the bass frequencies to the S1 Pro; and use the subwoofer's boost frequency and level knobs to adjust the bass sound. For my purposes, I keep the mid and trem controls set flat on the S1 Pro.