Counterpoke with armoured DB2 at all times.
Looking back on it, I wouldn't be surprised if it's 4-6 for Atom personally. Beetle shuts basically all of Atom's fullscreen tools down and has lots of tools himself which Atom can't deal with like air mobility and long reaching strings. Shield bash is really good against Atom since he can't really enforce anything after he blocks it and low profiling only gets you so far, especially for a move that either requires trait or does like 80 damage in the case of D3.
This is how you should probably play the Atom MU, just be wily as fuck and force Atom to make some hard reads. Get the life lead and keep it because Atom struggles to get it back is the only other thing I'd add to this.The way I'm going to fight Atom is standing outside of his range where his normals can reach me but mine reach him and just play reactionary and harass him. At that range if he makes a bad read on a projectile, low profile attempt etc he is eating a full combo and Beetle always has meter if he plays half decent so I'm bounce cancelling that into almost 500 damage on Atom or what have you. The risk reward is on my side in these matters.