For a sophisticated set up where you can map fuel for the individual gears, you are correct. For most folks on the street, running a pipe and power commander - and who describes himself as the average guy - you are taking things way out of context IMO. A PCIIIUSB only knows one map at a time for all four cylinders, and only knows throttle position and RPM. It does not care what gear the bike is in, or what gear it thinks it is in, or what the ignition is doing. The new PCV will change things for some folks who decide they need separate maps for each gear - but again, its an option that most folks will never explore.
Now, if we are discussing a far more sophisticated set up, you are correct to a certain degree. My argument would be why would you bother to run a TRE at that point anyhow... All that it accomplishes can be done in other ways or is not needed.