why use Atmel Studio?

no

but for instance just using arduino, going down and twiddling bits to toggle a pin gets you reaction speed of ~4us, using digital write its around 40us, 10x slower

at some point you are writing less arduino and more raw avr stuff, or you have a mcu that's perfect for your application but arduino does not support it

then you use atmel studio, I rarely use it, but knowing how to use it is nice