I have both Atom AR and LT hoodies and use them regularly with hooded shells. I really like the feeling of soft insulation in the neck area which the combination provides and find they fit and work well together.
I have a few different hoodies that I wear under a shell.
The hoods on all of the Patagonia hoodies are kind of like balaclavas and can be worn under the helmet and cover a lot of the face. If it cold enough to wear the Atom LT, it’s probably over the R1, and i have the R1 hood on. None of these hoods feel bulky under a shell.
I have a Patagonia Thermal-weight Capilene hoody(bit thinner than R1) and I find the hood bothersome under other layers. same with my hooded merino baselayer(very thin): it’s fine for active use where you have a maybe one,low collared, jacket over it, but with heavier, taller collars or hoods and multiple layers on ski shells, I find it less pleasant.