The fact you make it run within a browser don't mean you can't run it in a separate window.
The only good point I can think of is having a separate icon for the app in an alt+tab situation. But in my case I use the activities view on Gnome and usually view and recognize the window content. Also epiphany browser allows me to create "apps" with their own icon. Sadly not all of them work due to user agent nazism.
