Wouldn't an atomizer get a lot of surrounding stuff (for lack of a better phrase) wet in the process?
A bit, but normally you are putting down track first, so there is nothing except bare benchwork around it to get atomized glue on. I used a spray bottle that had been filled with Windex, and it worked great as long as the mixture was at least 45% or so water, and well shaken up. Spraying is fast and thorough - so it is preferred (at least by me) - and cleaning up the track afterwards easy with acetone and a rag is easy, etc.
In cases where I was working close to existing finished layout, I used a plastic squeeze-squirt bottle instead - a yellow one from the grocery store meant for mustard. This worked nearly as well but is not ultimately as fast.