It's not just javascript, it's also CSS (well, actually less). I disagreed with where atom put some of its controls, and I just put some CSS in to move them. It was easy.

I understand the question about "why use atom when st3 is perfectly fine?" (or for that matter, vim, emacs, etc). For me, it's primarily the plugin ecosystem. ST3's is good, atom's is better (and feels like it's growing faster but that's anecdotal, not data-based).

Also, in my situation (plugin-wise), atom is super-fast. My source files are usually less than 100kb, usually significantly so, though.