Buck Converting Voltage, to Switch Original Voltage
Yup that's fine. Just make sure the output of the buck converter to 5V is regulated well enough to not have too much ripple to cause the Arduino problems. 

It's not recommended to control the buck by the Arduino because if you don't do it right, you could fry the Arduino or cause it to power itself off. It is possible to do that though.

Easiest setup is to just get a separate buck regulator IC and have it create your 5V from the 12V line.