The device programming of fuses and other settings that can corrupt microntrollers it is best done using the atmel studio tools. 

If you need a prebuild, postbuild, preupload event where you want to define your own commands that is possible but it doesn't sound like that is what you need?

Hi, the word Arduino doesn't narrow it down enough because that covers so many different microntrollers.

Atmel studio was created by Atmel and it's license actually only allows for Atmel micro-controllers. That does include quite a few genuine Arduino mico-controllers but less so as the years pass. Atmel studio has a few stengths such as advanced device programming and the atmel hardware debugger can work slightly better than the hardware debugger in Visual Studio.

The atmel gallery is quite cumbersome for us to manage and the ide complicates life for arduino users by adding spurious (in arduino terms) files to projects. Therefore from a support and updates perspective Visual Micro it usually more update to date in VS than AS7. 

The Visual Studio hardware debugger caters for many more micro-controllers, is more mature (AS7 is actually Vs2015) and offers a lot of other development options.

It really is up to you though, if you have Atmel hardware and are an advanced user then Atmel Studio is a good choice.