When Tripleplay software is running it forced software mode. Yes- it’s a bad “feature”. You are correct in the way I use the hardware patches but one other thing is I have a few special hardware patches for fretboard splits.
In gigperformer I Use setlist mode and set a midi code for each “song part”. Sometimes Bluetooth interference prevents the program change code from getting to the Tripleplay hardware. For that reason I stopped doing transpose in the TP controller and instead do it within the rackspace. If I remember to turn off Wi-Fi and bluetooth on the phone in my pocket inched from TP then it’s much less of a problem.