Hi Dennis,
you can hack the x86 core really safely 
DFU is fully implemented in bootloader so the only chance to brick a board is if you want to modify if.
The ICSP header is only used to broke out SPI for shields, while the tiny 5x2 header is a jtag port compatible with any JTAG programmer (I personally use Flyswatter2 and it works great).
If you don't need a debugger and you are not going to hack the bootloader you can safely use the DFU upload procedure
Some interesting resources to get started:
https://github.com/01org?query=CODK
CODK codes are explained here