I dont think it makes much difference, I took 5v from near where the power socket comes in (the xedk power plug).
But he's using a max3232 and no zener diodes to limit the voltage, so he should connect it to pin 8, wich is 3.3v all the time.
Lets say you use the serial connection, but forgot to power-on the 360, you would be driving the chip with 5v which translates to 5v on the TTL/CMOS i/o too.