There are discussions about palettes receiving keystrokes when they are not in focus (and something that regards mouse events here):
I have a specific question about pasting, which is the most annoying thing I've noticed (yet) regarding the behaviour of the non modal window types. Ctrl+V puts the clipboard contents in the active document instead of pasting where the cursor is, in the textbox on the ScriptUI window.
Mouse right click + popup menu (Paste) is a workaround, but it doesn't prevent the accident of putting the pastboard contents in the document using the keyboard (you might not even notice). I'd like Ctrl+V to go to the Script UI window, when the Script UI window has focus.
Are there workarounds for this as well?
As far as I know, no, there aren't any workarounds for that.