Yes and then no and then yes-ish.
It will work with standalone ATmegas yes, but other MCU's no.
The libraries are written specifically for Atmel ATMegas, whether it's on an Arduino board or not.
Each brand of microcontroller has their own machine code.
Also, referring back to your original post, you can use a USB connection to program a microcontroller only if it has a bootloader AND is on an Arduino board.