I have the Ram flywheel, and a SPEC stage 2/3 hybrid disc.
It really should clear. That note, I was told, was for really old clutches that had very large hub springs. I have had no problems with mine as far as flywheel to clutch clearance issues. I also used ARP 12 pt flywheel bolts.
I did have a problem with the clearance of my stage 3 pressure plate to my bellhousing. I had to grind a groove in the bellhousing because the outermost edge of the pressure plate was hitting. I'm not sure if you will have this issue on a stage 2 pressure plate.
Good luck.