Is it possible to burn the Arduino bootloader into a stock atmega32u4 chip via USB? I know i can do that via the ISP but i was just wondering if this can also be done with USB.
Nope.
Some brand new 32u4s may have the Atmel bootloader pre-programmed, but I don’t think you can count on it.
I second the post about some chips coming with them preloaded and I have had very good luck with them. The price is often the same with or without the boot loader if you hunt around hard enough on ebay.