Just got my plate and case for an Atomic the other day.
And I've noticed the stabilizer issue, too. And I think I figured out why they're not working for Cherry stabilizers.
Backside of a standard plate with a cherry stabilizer:
Fuzzy backside of the Atomic plate with a cherry stabilizer:
Standard plate stabilizer cut-out:
Only image I have of my plate's cutout without being filled:
Anyway, the Cherry stabilizers have a little clip at the top that clip into the plate. The problem with the Atomic's cutouts is that there's a little notch taken out at the top, which is exactly where that clip would be holding onto.
Which since I've realized this, I might end up having to do some light modification and see if I can't just solder something in to fill in/provide support for the clip.