I had a Patagonia Nano Puff and I nicknamed it the wonder coat. So, I've got a lot of love for that one as well. To me, the Arc'teryx surpassed it for a couple reasons. Comfort is the most important one. The stretch panels make the coat super easy to move in. It's almost like it's not there. Also, I really like the hood on the Arc'teryx, it's so well engineered that it creates a comfy little pocket around your ears, keeping you cozy and blocking the wind. I also like the fit of the Arc'teryx better. The sleeves are more tailored and fit under my ski jacket better, making this jacket a great mid layer for frigid days on the slopes.
Speaking of frigid days, I visited Burlington VT during this year's polar vortex and lived in my Atom Hoodie the whole time. I layered it with a cotton sweater and a helly hanson warm underlayer, threw a scarf around my neck and was good to go. Temps were in the single digits and teens. If the wind had kicked up, I would probably have gone with a bigger coat, but luckily, that was never an issue. From a skiing POV, I wore my atom as a second layer on the slopes. Not sure what the temps were on the upper mountains around MRG and the 'Bush while we were there, I just remember that I didn't take too many pictures because every time I took my gloves off I was worried my fingers would snap off. Once suited up, I was cozy while maintaining a full range of movement.
By itself, the Atom is about the same level as warmth at the nano puff, but not as warm as the Patagonia down sweater (I have one of those too ;). Still like the Atom Hoodie the best out of the three. It's more comfortable and a lot more versatile.