Comma before end quote in bibliography
As others have indicated, style guidelines have to be followed, regardless of whether the reasoning behind the rules is clear. However, this particular example often varies by geographic region. American English grammar always places periods and commas inside quotation marks, while British English grammar is "conditional" - that is, they include periods and commas inside quotes only if it is part of the quotation, not the larger sentence. This site has an example and a more detailed explanation.   

http://www.quickanddirtytips.com/education/grammar/quotation-marks-with-periods-and-commas

Thus, it's possible that the style guide is based on American English grammar, while you have a different frame of reference and convention.