It amazes me that I can't actually find relatively few reports about our problem!
We have a Mac Mini and iMac that both boot from a Pagasus2 RAID through thunderbolt because both machines are used as a server! Since Apple does not make servers anymore this is actually our only solution!
We have the iMac and one Pegasus2 just purchased new from Apple and we could not select the Pegasus as Boot Drive for MacOS Sierra from out of the box! We thought at first that it was a hardware problem but after some googling we found out that Apple has switched off this option to boot MacOS Sierra from a Thunderbolt Drive! http://blog.frizk.net/2016/12/filevault-password-retrieval.html (Thanks for ruining our servers UlfFrisk)
Our new iMac came with macOs Sierra 10.12.2 and the new EFI so no solution for this setup! And for the Mac Mini Server, just cancelled the updates just in tIme and never switch off and hope there will be no power failure...
My question to Promise: "FIX THIS PLEASE!!!!!" so we can use our Pegasus2 as a RAID Bootdrive again!!!