One of the most important features of the new 4.2 software is the Model Axis. This new feature in the 4.2 software allows you to correct the base of the model when the user does not image properly. You should always start imaging from the occlusal and finish imaging from the occlusal. If you don't, you will get a funky "model box" like you see below. If we look at the model axis step, you will notice that the model is not correctly positioned in the model axis. What you need to do is adjust the model axis and the base of the model will appear normal.
Your proposals will be better and you will experience less headaches in design if your model box is proper. So whenever possible, image on the occlusal and finish imaging on the occlusal. Then simply adjust the model axis as needed so that we can go ahead and have a proper model to design our restorations on.