Hookshot does allow customization of the positions of the window throw (and long throw). You can create a custom shortcuts in the wrench and ruler tab, and then select the custom shortcut from the configure button for the window throw, at the end of the list. I realize this can feel a little hidden in the UI, so I'm planning on making it a little more straightforward in a future release.
The custom shortcuts in Hookshot are beyond what I've seen in most apps, especially since you can customize what happens in repeated executions of the custom shortcuts. Let me know what other apps out there have the customization that you are referring to.