I figured it out!
I just finished installing my hybrid kit.
If you look on the back of the back plate, there are several of these foam "dots". This pad is meant to have the foam dots 'break away' and use as extras in case any of the 'dots' fell off of the back plate. They give extra clearance for the back plate and the back of the video card so it doesn't short it out. They are nothing but spacers, and if they didn't fall off of your backplate (mine didn't), then you are fine.
Case closed fellas! We did it.