So today I've noticed that the option to create a chrome shortcut has changed and no longer includes the option to "open in a window".
This is annoying to me as I liked to create Web apps on my task bar, so although you could now create the shortcut, it would open in the main chrome window as a tab instead, which destroys the concept as using it as an app.
I did find the solution, they've just moved it.
So for now, what you need to do is the following:-
- Three dots and create shortcut. It will then create the shortcut on the desktop and start menu.
- In the chrome address bar go to chrome://apps
- Right click on the desired app in the chrome window and choose "open in window".
- The shortcuts should now open in their own window just as before.
Hope someone finds this useful.
Edited to add: Chrome 70 beta. The option still appears in 69, which hints that it may well change in the imminent future.