Do you know exactly what Japanese transmission model number they are talking about installing? Possibly an Aisin AX-15? If so, you'd be fine with that transmission.
By the way, the transmission should never be left in Neutral for flat towing because it is not supposed to spin while you are flat towing the Jeep because the transmission does not get any lubrication while being flat towed. For flat towing, the transmission is supposed to be in gear, like 1st for a manual or Park for an automatic, with the transfer case in Neutral. You can confirm this with your Jeep's owners manual.