It sounds like the standalone is trying to open in a fullscreen resolution that your display doesn't support. When the game opens and your display says Out of Range, try pressing Alt-Enter to force the game into windowed mode, and then if you can see the game, enter the options menu and set up your desired resolution.
In order to force the game itself to start in 640x480, you will need to make sure you're setting the properties on the game executable, and not the launcher. The executable is called tmi.exe and should be found in the TMI installation directory (by default this is Program Files (x86)\RedBedlam\The Missing Ink).
The standalone version is still built with Unity, but should run a lot better than the browser version. You may suffer a few hitches initially when you enter a zone and assets are loaded in, but after this the experience should be relatively smooth. What are the specifications of the computer you 're using to run the game?
Also, depending on where you're accessing the game from, you may also be experiencing a higher-than-average latency. There is an option in the settings menu to show your latency on the top bar; anything above 200-250ms, or a fluctuating latency, will start to noticeably impact your gameplay.