Have you seen any of Pogue's books written for the various Apple Mac and Windows operating systems? The format he uses is very easy to follow. When he is discussing some difference, the text changes, with a highlighted box for each, with the information that would be relevant for Unix, and in the other, for Linux.
As for the different software installations, then why do you hesitate to break that chapter in your document into two parts, one for each system?
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