One thing that's frustrating, however, is that I use KM inside an application whose window is resizable but the graphics are always top-right justified. So, for this app, I'd like to have all mouse actions refer to the Top Right of the Apps window as apposed to the default which is Top Left. I manually have to adjust it so it looks like this:
Is there a way to record macros where I can ask KM to always reference Top Right?
No, there is no way to set the default recording to be “top right”.
However, when recording, Keyboard Maestro records both the click and the window and screen information, and so you can change the click reference location in the recorded action and Keyboard Maestro will adjust the coordinates to match. This information is not saved permanently, so you need to make the adjustment fairly promptly (quitting the editor, or a macro sync from another Mac would lose the information).