I feel like a moron and after I worked through my issue I did find some references to it on the web but wanted to put my two cents worth in at a place where it might do some good.

When I had trouble inserting and removing my hard drive caddy's from both of my new Atomos Ninja's I thought the problem must be that I didn't have the screws tight enough and the ends were catching on the sides of the slot.

When tightening the screws only made things worse I had to think things through. It finally dawned on me that I might have the opposite problem. That tightening the screws was causing the caddy to flex or bulge in a way inhibiting it from working correctly.

Sure enough a couple of turns loosening each screw caused the caddy to easily slide in and lock into place in the Ninja and then easily slide out with the release button depressed. Whew!

I took the added precaution of deepening the countersink holes slightly by rotating a countersink bit a couple of turns by hand in the screw socket. Since then, no problems.

I agree that distortion due to over-tightening is the problem rather than protruding screw heads - though it seems to be very easy to start the screws on a cross-thread. They are a loose fit in the thread.