Wanted to update this thread.
Some more information: In addition to the "loss of punch" I mentioned in the OP, I also quit using pedals at all because I noticed a difference (for the better) in my clean tone when I went without my board. I don't use a lot of effects; my old setup was EHX Bass Microsynth - VT Bass v2 - Digitech Bass chorus.
I bought a VT Bass DI thinking it would be like my other VT pedal but with a blend, but they sound different to me. I like the sound of the VT Bass v2 pedal better, except it was too compressed ("loss of punch"). My lackluster results with the blend function of the VT DI are why I hadn't really looked at parallel signal chains.
The Brimstone XD-2 is a super cool pedal, tons of different tones possible - however I spent a some time with it and the low end still sounds a little "flabby" to me even with the gain way down. Might just need more tweaking of the 11 knobs on the thing

May put it up for sale.
SO - I picked up an Xotic X-Blender from the TB classifieds

I went back to my old setup but ran the three pedals through the parallel loop on the X-blender. Also added a TC Polytune 2 tuner - my old Korg Pitchblack Poly was picking up some weird noise interference while tuning, and I never really liked it anyway.
So far this setup sounds like what I was after. I have my effects blended with clean to keep the "punch" and when I run totally clean I am "true bypassed" around the effects pedals for no "tone suck".