I already had the EMSCRIPTEN environment variable in there, so it appears that your first suggestion was the one that did the trick. It only showed up in the “Project Launcher” dialog and not the “Launch” dropdown from the main toolbar, though - is that intentional?
Despite all of this, I now get an emscripten error for both and Chromium builds. Log file here: http://pastebin.com/HRH5sD7w
I can add this as a new question if you like, though.