I'm having trouble deciding whether or not...
I'm having trouble deciding whether or not to get the version with the hood or without the hood - does having the hood cause any problems when you add another outer layer on top of it? Would you need to have both hoods up or can you have the hood on the Atom LT down and the hood on an outer layer up?
I've always found that a layer with a hood is a pain in the butt. In a down item like this it is easier to stuff it down. But, if this is mainly for layering, bag the hood option.
I've used the Hood and jacket version of this. I find it depends a bit on the type of hood on your shell. If it's a storm hood, where the collar and hood are one, the Atom LT hoody works great. I give it a couple inward rolls and it forms a soft gasket and doesn't choke me. For drop hoods where the hood and collar are seperate, a jacket is more comfy.
I prefer the hood for wearing the Atom on it's own in more mild weather or when I'm moving in chilly weather or when it's snowing.
Take note this is a synthetic insulator not down, as indicated by JP.