Line 1 by itself allows the domain to use the GetImage and CopyArea core protocol requests on all application windows, allowing their contents to be captured. This is the mechanism used by the GIMP application's window capture feature. However, there is a ``back door'' method for capturing contents: create a window with no background, which causes the windows beneath it to show through, and then copy its contents . Line 3 allows the application to create such no-background windows; denying this permission would prevent their creation.
The three capture methods described here are the only ones the author is aware of in the core protocol. There may be other methods available through extensions; it is hoped that the copy permission will cover all direct capture methods while transparent will cover any indirect methods such as alpha blending or translucency, which are becoming common.