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Can i customize(change colors, the shape) the windows/boxes,that are shown below:

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Where those settings stored in CSS?

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You can not freely change the dialog;

It is a normal GUI window of the program gksudo.
But depending on your needs, it may be good enough to customize the gtk theme for that window. That would not allow to change the window's shape, but supports various changes in spacing, fonts, colors and sizes of UI elements (it may not be easy to do).

You could possibly find an alternative to gksudo to replace it, though.

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