You retract to 3 inches and the torch is crashing on rapids because of warpage? We cut 20ga, 16ga and 12ga all day long. I have safe Z set at .5". That means that when the torch shuts off, it retracts to .5" and moves to the next start point, probes and starts the next cut. These Z moves are relative to the work piece as the THC keeps the torch at set height above the work. I use G31 for probing, not G28. I'm not sure why you are needing to command a rapid down to .5" before beginning the probe...or more to the point, why you have the need to raise the Z so high for rapids. You should be able to retract to safe Z (.5" or less), move to the next cut and call a G31 to probe for the next pierce height.
You shouldn't be getting that much warpage on 16ga and hardly any at all on 12ga. What are you're cut speeds and plasma power settings?
"Stay at your safe +5 inch height then do a rapid probe down to find the surface then raise .5 inch above that point and reprobe in slow mode for a more accurate height setting."
Maybe I don't understand the problem. Why would you need to retract to 5" for rapid moves. Moving up and down 5" at each cut would take forever on multiple nested cuts. Even on 24ga steel, I've not seen more than about 1" of warpage and that's rare. There is only one part we've done where the Z range was about 4". On this part, I had to bump safe Z up to 4.5". This was not because of warpage, it was due to the shape of the base material being cut. even then, if the Z was at the 4.5" rapid height and the cut was at 0", the G31 just probed down to the material. No need to command a rapid down before beginning the probe routine.