What happens when you crank the engine but the transmission is not in neutral? Are you applying torque to the transmission? Should the vehicle always be in neutral when turning the crankshaft manually?
Many vehicles have some type of safety feature to prevent people from doing this. (eg: Press the clutch all the way down before cranking, etc) If this is the case with your car, then it is identical to cranking it in neutral.
If you don't have such safety features in your car, the car will try to launch forward and the engine will stall. Same as if you would take the foot off the clutch and not give any gas.
I am pretty sure you cant crank(the car won't let you; you can turn the key all you want, but the car won't send any power to the starter) when your transmission is not in neutral or park. Heck, in my car I can't even take the key out if transmission is not it "Park".
Assuming that you have somehow managed to defeat any modern safety features then, yes, you will be turning the transmission. The starter motor will engage the flywheel and will try to turn the in-gear transmission using electrical power alone. If you are in a low gear, there is an excellent chance that this will cause the car to jerk or roll forward.
In the days before the "clutch down to start" safety features, this ability to move the car with the starter motor was described in driver education classes as an emergency way to move the vehicle in a dangerous situation. The classic example was "what if the car stalls on the railroad tracks? Leave the car in gear and turn the key."
These days, when asked the same question, the instructors usually say "Get out of the car before the train hits you, idiot."
In a traditional, manual transmission car, the car will physically try to move forwards. In a low gear with the parking brake off, the car will slowly roll a short distance (before either starting or exhausting the battery). This can be a lifesaving function if the vehicle looses power and breaks down in a dangerous position as you can effectively "drive" the vehicle to safety (albeit very slowly).