The problem is the inconsistent behaviour of different API functions.
For example, as Grahan mentioned, you can apply the scale in calls to Rect.Contains functions, alright.
On the other hand, GUI.Button works fine without modifying anything - clicks on the button are captured correctly.
However, using GUIStyle with normal/hover texture backgrounds, does not work correctly, and you have none control over this.
And it seems that in version 4.3, this is all fixed and everything works as expected. Have to double check that though.
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