Ed,
Let me start by saying that I have been forced to learn about Allison fluid and now consider myself to be somewhat of an authority.
In December of 2008 I had a company in Texas called RV Mobile Lube come out and service my unit, including a transmission fluid change. The long and the short of the story is that the coach never moved (until the tow truck came) after they drained the transmission. Later, when I measured it, I found 23 quarts total in it. That is after they had added more when the first testing proved futile. I am currently suing them for the damage that I believe they caused to the transmission.
My C-12 has a shallow pan. I am not sure about yours. Allison made them both ways. A shallow pan is 2" deep and a deep one is 4" deep. You can also call Allison with your transmission serial number and they will tell you which you have.
There is additional oil in the inter-cooler. It took 44 quarts to refill my entire transmission after it was repaired. Allison says it should take 40, so 4 quarts are outside of the transmission.
Allison says that a deep pan needs 39, as you stated, but a shallow pan only needs 31. On my coach, I would add the 31 to the 4 and come up with about 35 quarts for a refill.
Yes, it is OK to be a few quarts low on start up. No, it is far from OK to be real low on start up. The Allison bulletins tell you not to use the dip stick as a measure when filling. I can tell you from hard experience that is good counsel. Until the fluid is circulated in the transmission by the charge pump, the dip stick is useless. The specific procedure they recommend is to measure the fluid removed. Throughout the failure, my dipstick showed overfull but when we drained and measured only 23 quarts came out.
If you are low you will burn up the charge pump and you can kiss 10 grand goodbye. If you over fill, you will not damage the transmission unless you run it hard before you adjust it back down. You might also make a mess if you overfill as it does have an overflow port. At the first start up, immediately put the selector in D then R. If you do not feel it engage, shut it down and rethink! You will need to idle it in D for a few minutes to warm it up enough to get an electronic reading.
I think I would go to the full refill number for the transmission(31 or 39), at a minimum, before I started the engine.