A feature to Turn On/Off the Alternative Input (perhaps as part of the Input section) would be great, especially if it did not require the use of the Stereo Loop or a Stomp/Effects block to make it active. The idea here would be to use a Stereo source, say a guitar with Magnetic and Piezo pickups, and insert them into different locations in the Rig.
For instance, the Magnetic pickups could go through the Main Input on the Front of the KPA as normal and use any of the Stomp, Stack, and Effect available features; the Piezo could be inserted before the amp, but after a Comp, Boost, Distortion Stomp section or perhaps after the Stack (no amp) and yet still take advantage of Mod, Delay, and/or Reverb in the Rig.