Good question. The answer is yes although some of this will be possible also in VS
The VS solution is currently better, the intellisense and code explorers of vs are better but I think Atmel will continue to improve.
Atmel have said they would like to help create scripts to allow advanced users to migrate from Arduino to raw AVR/ARM however this won't be considered further until we have a stable period of Arduino compatibility. This helps keep the support problems for me to a manageable amount.
Furthermore there is no reason why we do not have half way houses, part Arduino and part not. The Atmel Studio project property pages (tool chain) are quite well designed for this purpose.
In the current system you can break out of Arduino in various ways and of course you can always use AVR syntax in all arduino projects.
This is a big topic, it would help if you describe you objectives and which parts you consider to be "arduino compatible". Remember that your hardware has the arduino bootloader pre-installed, will you be dumping that and cleaning your chips?
Examples of what you can already do:-
1) Disable auto generation of prototypes
2) Compile without using the arduino core (see APM SITL and HAL examples on visualmicro.com, also see the advanced board configuration properties). the SITL example is a great example because we compile a program using cygwin that runs under windows. However, I do not provide support for this because users are expected to know what they are doing
So what do you want to do? Use your own libraries instead o Arduino? Work without the arduino code? native AVR????
Thanks