Is the empty GI tract a hollow tube with air inside, or is it generally collapsed until food is eaten?
Under normal circumstances the stomach and GI tract have very little "gas" in them - whether it be flatus, air, CO2, or anything else - and so are essentially collapsed with the walls against each other. However, gas is continually being produced by the microorganisms that inhabit our gut, and can also come from swallowing small amounts of air, fizzy drinks, etc., so the environment is never 100% gas-free. A typical person produces on the order of 500-1500 ml (0.5-1.5 liters) of gas per day.

If you're interested, the Wikipedia article on flatulence is a good introduction.