Atmel studio 7 vs Arduino IDE for register level coding?
I actually wouldn’t recommend either for professionally developing for Atmel chips. Although Atmel Studio is a nice enough IDE (the simulator is amazing!), it does make it very difficult to unit test your code or to set up a build server. I would personally recommend you set up a Make (or possibly CMake) based setup directly on top of the avr-gcc tool chain and then simply use the text editor of your choice. 

As for learning about programming against raw registers, I have to recommend Atmel Studio and one of their XPlained evaluation boards. Atmel Studio includes a simulator that actually shows you, bit by bit, the current state of the registers.