Chiming in for success. I finally found a spot in between projects to take some risk with getting this to behave a little more normal. Previously I had to boot, turn on Apollo, restart, rock on.
I tried SSDT V2 today and edited the SSDT as suggested.
When booting with the device on I can turn it off and on like any Mac and its a beautiful thing other than system profiler but thats just cosmetic.
When turning Apollo on after the boot I get the "multimedia device icon" on the tool bar. It's not actually connected at this point but if I turn off and back on the icon goes away and the Apollo connects and is able to hot plug. (Note: does not work after shutdown. You gotta get the TB card running and then you can restart away, device on or off.)
Thats progress to me. Thanks for the read and help friends.
Next test...during my build I found that "Enable USB" in the TB Bios settings hung up my boot. Lets see what flipping it does now. EEEEeeeek. Advice or explanations are welcome.
UPDATE:
Requires an initial boot with device on and restart (noted above).
After that you can hot plug away. You can turn off the device, restart computer, turn on (twice here but whatever), and hot plug more. Plug your hot plugs in all the hot...plugs.
As for Enable USB in TB Bios, yeah that crashes the **** outta everything. Any ideas?
Note: I realize that all of this has been said but the redundancy can be helpful for readers so I'll leave it.