Allison with Transgo Jr is still stock. All the trim valves do is divert an extra 120 psi to the C3 and C4 clutches; nothing more and nothing less.
Unless the definition of stock is not opening ANY of the powertrain's components to make any mods, I agree with you Mike.
If the argument is tuner, intake and exhaust only, then by rights a jr is not stock. But that's an argument that can go on for years in itself.