This has been requested before, and I've given it some thought. The problem here is that you are only changing the shortcut's icon, not the application's icon. So, for example, if you change the shortcut icon on the taskbar, and there is a different shortcut icon in the Start Menu and a different one again on the desktop, which one does DisplayFusion use? Also, some applications have different icons for each window in a process. So should the custom taskbar shortcut icon override all window icons for that process, or only the "main" window?

Pinning is coming in the next version, I hope to add it around Beta 6 or 7 next month.