Well I felt so good about things that I decided to do my friend's build with the same motherboard (GA-Z87X-UD5 TH)..
As mentioned before - I decided to go with Mountain Lion instead of Mavericks for my friend's build, but so far I haven't been able to get my Apollo to show up.
I went back to the other machine I had build which is running Mavericks to see what other differences there may have been.
To my dismay I found a few weird things happening with my Mavericks build which I thought was successful:
I've found that whenever the Apollo is connected, the spotlight icon in the upper right corner is no longer visible. Also the spotlight short cut (command-spacebar) no longer works. I attempted to take a screenshot of the situation, but the shortcut for that doesn't seem to work either (command-shift-4).
Actually it looks like the spotlight icon appears in the form of an intermittent flash which appears for a split second once every minute or so.
Although the two OS X shortcuts seem to be disabled when the Apollo is connected, the Finder-related shortcuts appear to be working as normal.
If anybody else is having an Apollo working on their setup without exhibiting these issues, I'd like to know what settings were selected in the BIOS - particularly in the Thunderbolt section....
Man, I'm really starting to miss the Z77 Motherboards with Thunderbolt!