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the onboard LED is not actually connected to pin 13. The board is set up so that when you call to pin 13 in an Arduino sketch, then this controls the onboard LED too (this was done so that the Blink sketch would work out of the box.)
If you want to control this LED through sysfs, then you need to write to gpio3. no muxes need to be set for this.
echo 3 > /sys/class/gpio/export
echo out > /sys/class/gpio/gpio3/direction
echo 1 > /sys/class/gpio/gpio3/value
arduino_4_life do you know where in the source code for the Arduino IDE (the version for Galileo) this alternate path is taken? I've been through all of the x86/cores/arduino code as I'm trying to figure out how a call to digitalWrite(13, HIGH|LOW) would be disambiguated.