Don't worry, I was surprised at the size of the dipstick tube the first time I saw it. Even more surprising is the length of that thing (along with the one for the tranny). It expands inside the tube so you will have to turn that handle a couple of times to be able to pull the dipstick out.
You're right, diesel don't like air, but that's in the fuel system. Rest assured that you can pull that dipstick out without fear. Obviously for the most accurate measurement you're going to want to do it when the engine is warm, but not running.
My bus holds 20 quarts. Yep, that's 5 gallons of oil per change. You should try and find some documentation with yours to see what it takes. Otherwise I would just drain it and start adding oil, check with the dipstick, add oil, check with the dipstick, etc until you get to the full mark. It should also be noted that this thing isn't like your car. One quart is just a drop in the bucket.
I wrote a reply explaining how I figured my fuel mileage, but it seems to have been swallowed by the intarwebz so I will just tell you that my 6.6 gets 8 mpg and that's what I hear from all kinds of people with the same engine, regardless of configuration.