According to the SRM page 94:

DO NOT APPLY VOLTAGE TO ANY I/O PIN WHEN POWER IS NOT SUPPLIED TO THE 
BOARD. 
IT WILL DAMAGE THE PROCESSOR AND VOID THE WARRANTY.
NO PINS ARE TO BE DRIVEN UNTIL AFTER THE SYS_RESET LINE GOES HIGH.

I hope to have a deeper understanding on that statement. Does that only 
apply to specific pins such as the boot config pins?

My application requires beaglebone to be a secondary processor and it 
communicates with the primary processor using I2C and SPI. The beaglebone 
will bootup and shutdown occasionally while the primary processor will be 
on all the time.
I am under the impression that the pins on the beaglebone should be on high 
impedance when beaglebone is powered down. With I2C pulled up by default 
and assuming I did attempt to drive the SPI bus when BBB is powered down, 
is that going to destroy the processor?
 

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