At first glance, this does seem odd, but if you try out avrdude-6.3, you'll notice that it doesn't actually successfully flash the microcontroller on the Arduino Dock.
I can't recall the exact details but the avrdude developers made some changes with how GPIOs are accessed and it doesn't work on the Omega.
The last time it worked properly was in version 6.1.
Changing the version in the package makefile to 6.9 was our attempt at making sure our version (6.1) gets installed instead, but it turned out to not work...
We've reverted the change and if you do ./scripts/feeds update onion in the build system, it should build properly.