My understanding is that Resharper (8.0.1 as of this answer) does not pay any attention to the _references.js file. It analyzes the project for any/all available javascript files and provides Intellisense accordingly. One important thing you lose with R# compared to VS default functionality is the ability to reference remote js files, eg:
///<reference path="http://whatever.com/your.js" />
will not work. Currently it's a known bug with no scheduled fix.