In the [x] science mod, the right click and the left click on the icon in the toolbar could open different mod windows.

Same could be done there:
the left click opens the main SM window (as it is now), but the right click on the icon open the most used by user Transfer window, for example, the Fuel Transfer window.

So if I am using Fuel Transfer window often, I could just right click on the SM icon in the toolbar.

Implementing for release 6.0.6.0. Behavior is as follows:

left click opens Manifest window. Manifest window now remembers resources selections. if resources(s) are selected, Transfer window automatically opens.
If you close the manifest window with resources selected, the Transfer window will remain open.
Right clicking on the App Icon will open and close the Transfer Window IF resources are selected.