Here are my answers:
1. For V/H Cylinders, your input depth is just the maximal depth for the sprite, 3DNes will automatically calculate the real depth. That's why you see the difference between the depth you entered and the real depth after math
2. The situation is not very clear for me. Need more infos.
3.Click the intended cube and press Adjust again. It will not intended anymore. There is no difference between Cube and Full Cube for the moment. It's reserved for future development. It applies also for Unknown and Char.