For example, because the app restores its state and you have a few "projects" within the app.
> I'd rather see things grouped by project
Ok, and what if that project is encapsulated in an app window? Why introduce an extra level of indirection for no reason and spend time configuring it? If you frequently need a set of "5 firefox tabs, 2 terminal tabs, 4 text editor tabs, each in a separate app window", sure, spend time tagging it, set it as a WM project and launch/activate it with a key, but not everything is like that.