Well, for starters, you check the fluid on allisons with the bus running and in neutral. So if you're checking before you start it, that's your issue. Check it with it running.
Second, fluid level can vary on the dipstick based off of temperature. They'll either have 2 crosshatch areas for both cold and hot fluid temps. OR one crosshatch area for hot fluid. If the fluid is cold and not in the crosshatch area, I typically wouldn't worry, so long as the level is on the stick and not in the "add" area.
The only "phantom" place a transmission can leak is through the cooler, but the lost fluid will appear into the coolant. ATF floats on the coolant, especially several quarts, so if the reservoir and radiator aren't overfull and show none, you can rule out the cooler leaking.