Is it possible to disable "Show method separators" for JS? OR Enable only for PHP files?
It works perfectly good for PHP:
But in JS it makes mess
Nope, this setting is currently global for all the languages. Feel free to submit a ticket in tracker (see below).
By the way, here's a ticket about JS separators: http://youtrack.jetbrains.com/issue/WEB-3855. Feel free to watch or vote.