the newer allisons have a 'auto neutral' wire going into them. it is exactly for the reason yoiu say.. a lift deployed.. on a utility truck it does the same if the boom or bucket is deployed..
this is the body builder book...
http://bodybuilder.navistar.com/Gene...0000003601.pdf
wiring diagram 12.8 shows the wheelchair lift and shift inhibit relay.. i dont know where thje physical relay is however it looks like grounding the violet wire from that relay (perhaps at a diode if thats still there) will engage the relay and probably allow you to shift.. or you can jump the wires on pins 3,4 of that relay together (remove the relay) and same occurs..
the other way to do it has have someone with allison doc disable the auto-neutral wire in the transmission TCM..