Linux newbie here, but after ~6 hours of searching the internets I finally found a solution.
1. Pair device(s) to Linux
2. Pair device(s) to Mac OS X
3. Run the attached script in Linux
Note: The script is assuming the OS X disk is mounted and its name is Macintosh HD. Change 10:9A
D:7E:10:E2 to the MAC address of your Magic Mouse or Magic Trackpad. The script will work for the wireless keyboard and the Magic Mouse or Magic Trackpad. Any device not paired with OS X will be removed from linux.
After rebooting from linux the keyboard will not be paired during the boot process. If OS X is your default boot option just let it boot then reboot and you will be able to use startup keys.
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