I think I get what you're saying. I'm not too worried about that, though, as it will be such a tiny fraction of the sound after it's been through an overdriven preamp and EQ and stuff. Again, I'm only concerned about preserving the immediate attack - routing that around the pitch shifter and everything below whatever Hz or initial attack (if I use the compressor method suggested above) will be routed through the pitch shifter.
Anyway, looks like this is a pretty niche need and no one's actually tried it, so I guess I'll be the pioneer here and report back after I try a bunch of different things out :)