You want your amp's ground to go through that pickup if you were to "do it right". Outside of that there isn't anything else you can do unless your vehicle is one with an override. Most of the SUVs and trucks (not mine) will leave economy mode and go into charging mode if you manually turn on the lights or on models with a tow button if you hit the tow button. Those are the only two tricks I know of.
With these vehicles you really only have a few options. Get AD based alts (which is what the HO alt companies should be suggesting) and deal with the charge warning, go with externally regulated and deal with a charge warning, or get an MLA. For the record I bought an MLA last year, just never got around to putting it in, should have it in next weekend though finally. If I were you and if you don't already have an HO, get an AD based alt instead and just deal with the charge warning on the dash (tell the alt manufacturer what you're doing and they will give you instructions on how to wire it up).
In reference to your voltage... It's walking right? By that I mean one minute (it shouldn't be constantly moving every second) it's sitting at 13.2, the next it's at 14.1, then 13.6. then 12.8, and so on? If it's going from 14.2 to 13.3 when you turn it up then it's drop, not the PCM... The alt should still provide amps no matter what the voltage is. I have next to zero drop even when in economy mode (12.8-13.2).