The major difference between the citation styles in the Chicago Manual of Style and the U.S. Government Printing Office (GPO) Style Manual are caused by the needs of the users of the two style guides.
The Chicago Manual is geared towards the commercial publishing market detailing the layout of books and articles, page numbering, citing from various sources and word and punctuation usage. It is a comprehensive reference work, running over 950 pages in length.
The U.S. Government Printing Office (GPO) Style Manual is half this length. It has comprehensive sections on punctuation, capitalization and word and sentence structure. It also contains sections covering areas fairly unique to the publishing needs of federal organizations.