IIRC, for a game that uses pixellated graphics (point sampling), high quality fullscreen and low quality fullscreen will have a similar appearance (unless there are text objects I think, but having text objects in a pixelly style game is unlikely), so the low one is the way to go.
other than that, if your game uses node webkit, I would suggest doing a launcher that , if fullscreen is chosen, change the monitor résolution before launching the game (in kiosk mode, as in that case you do not want the users to be able to quit the fullscreen mode, which would actually work similarly to older PC games), and that will change it back afterwards, not sure why this is not actually supported by node webkit.
if your game is for the web however, not sure there is a solution other than suggesting your users to do so.