Thank you - I did a bit more troubleshooting. After doing some (potentially unrelated) graphics card troubleshooting I made the BIOS settings changes that you suggested. I had already replaced the OsxAptioFix2Drv file with the 2000 one, but despite this fix OS X would not boot. I then went back to USB3.1-enabled in the BIOS and the Apollo was recognized. I realized later this was most likely because I am still running El Capitan, and you mention in a previous post that it was not necessary to enable Intel Thunderbolt in El Cap.
Unfortunately when I restarted my computer the Apollo is no longer recognized despite the fact that I didn't change any settings from when it worked and the firmware installed. Upon booting into Windows I don't see the Apollo listed in Device Manager anymore either, though the BIOS still shows that PCI-EX3_16 has a Thunderbolt device installed.
Do you think it might be worth updating to Sierra in this case or continue troubleshooting in El Cap?
Thank you very much for your help!