I dropped this for a bit, but came back to it in the last few days. I finally fixed the issue with MacBook Airs. This fix assumes that all devices have a Wi-Fi network port. I feel this is a pretty safe assumption in 2017 even with older Apple devices. This also assumes that identifying a device by Wi-Fi mac address as opposed to ethernet mac address does not adversely effect how CloneDeploy treats the device.
I checked to see that the osx_task_list script looks at all mac addresses on a given device before determining if a task has been assigned to that device. Since this is the case CloneDeploy should check for active tasks for Wi-Fi as well as ethernet which means that it should not matter which mac is the primary identifier.
Next I went back to the osx_register script and changed the entry in line 9 to
mac=$(networksetup -listallhardwareports | grep -A 3 "Wi-Fi" | grep "Ethernet Address:" | cut -d " " -f 3)
This will now choose the Wi-Fi network port as the primary mac address when registering a new device. So far in testing it has worked properly.