I was actually able to install Windows 8.1 Update 1 on the mSATA drive as the system drive and the second one, at the 2.5" slot was identified on the installation. But then after shutting down once it simply did not recognize the drive anymore.
I uninstalled the Intel RST app and changed the BIOS setting to Removable Drive and it started recognizing again but then had to shut down the NUC a few days later and the drive disappeared again, very frustrating!
Is this a BIOS compatibility issue?