Is the Arduino bootloader really the Atmel bootloader? Can I use Flip to upload? I've been asked to do a small project using an Ada BlueFruit board. It has a ATMega32U4. The 32U4 comes from the factory with a bootloader pre-installed. I've never used an Arduino before, but I have used AVR a bit in the past. Is the Arduino bootloader actually the one that came pre flashed from the factory? Does it even matter if it's the same bootloader as far as Flip is concerned?

Can I use the Flip batchisp utility to load my application code? We don't have a programmer handy and I don't want to muck up the bootloader on the board. 

It's my understanding that the Arduino IDE tool chain does a bit of preprocessing "behind your back". I'd much rather continue writing straight AVR code in Atmel Studio. Is there anything I need to take into account when writing my application code? For example, do I need to do anything when compiling my app code, or when uploading it, to ensure it doesn't try to write to the memory addresses in the bootloader's range?
Arduino uses a different (second) bootloader, next to the DFU one that build into the 32u4.