The config doesn't have a bypass, nor a manage anything within it. Are you sure you're looking at Expert Mode of the config? It's a button on the bottom-left of the Wizard version of the config.
That being said, you should make your computer's default soundcard one of the "Breakaway Pipeline" soundcards, reboot the computer to make sure that nothing set to use the default soundcard is still using it. Then you can try setting the soundcard, and optimizing latency, in Expert Mode config. I highly recommend "KS" Kernel Streaming to access the soundcards, as you'll be able to get lower latency and ~guarantee a 1:1 bit accurate output from Breakaway's (multi-phasic adaptive) SRC (or you could use it without SRC, but I can't recommend that, even though I don't use it myself).
For some settings on a large-scale system…
preset: Reference Movies
range: 25 (higher if your input is less than -18 LKFS)
power: 100
speed: 15
Try Reference Jazz if it's still too processed sounding. 🙂 I used to "run" a 180kwatt Turbosound setup, so I recognize that even with these settings, it can potentially effect impact. REAL punch 😉 not the complete opposite that most people call "punch" these days. But those settings should be pretty bangin'.
Please send pics of Breakaway @ your FoH with a sightline in the background some time. 🙂