Dick,
I have the same vintage 4000MH in my coach and have experienced the precise situation you have described. With transmission at operating temperature, on level lot, with countdown completed the Allison control panel would read low 4 quarts. Allison assures users that the panel is accurate so I add a gallon of fluid and check the panel next time I meet all the requirements. Result is still low 4 quarts so I check dipstick which shows I am over full. I removed three quarts and now get panel reading of 3 quarts low.
So, I am convinced that the Allison control unit is not reporting correctly or the level sensor is not reading correctly. Until I can get the coach in to an Allison shop I will use the dipstick. It is bad to run over full.
Good luck.