By adding a PTO....what did you add? It is my understanding that allison's have the PTO cover plate but may or may not have the gear in it. By that I think the option shows the tranny with or without PTO gear? You may have a manual trans though?

I have a 4500 that has the MHE 2350 trans with gear and of course, I have the dash switch. The cruise control buttons can alter speed after turning on PTO switch.
Sorry about what EFI Live can do......don't know. I do know that in Scan/DTC I cannot activate the PTO light, so chances are EFI Live don't even see the routines?

BTW mine is a Diesel and I see you posted in the Gas section, so you may have the 8.1 gas engine?