If your referring to the popup that offers to show you the method to set your raid to native mode when
you uninstall the Intel Rapid Storage driver suite, you can just ignore it. Just click no.
Restart and install the new rev Intel files asap, then restart again.
So, you say the 1.3 Intel toolbox shows it will support your SSD even in raid pass thru mode. Good.
After you have installed your new IRST drivers check to see if the Intel app starts in the tray after boot up. ( no yellow bang )
If you see the bang you can start the app via the tray icon, the full window will open and the yellow bang will change asap.
I imagine Intel is fixing this problem soon.
Hope this helps.