Q. Could CMOS weigh in on the proper placement of punctuation in relation to quotation marks when the quoted material is an abbreviation that will be used in the document? For example: This agreement is entered into between Corporation X and Agency Y, individually “Party,” and collectively, the “Parties.” The typical rules would suggest the above punctuation is correct, but the abbreviations are technically “party” and “parties” (not “party,” and “parties.”). Would these be exceptions?
A. No, those wouldn’t be exceptions. In a style like Chicago’s that puts commas and periods inside closing quotation marks, the punctuation is assumed to belong to the text and not to the quotation. This convention, though it has its drawbacks (your question reveals the main one), has the advantage of allowing commas and periods to stay with the words they follow instead of getting separated by the width of the quotation mark. Consider also that there’s no such thing as a party, or parties. (with the comma or period attached).
For a more detailed look at this convention (and its history relative to the alternative British practice, which does put periods and commas outside closing quotation marks, though not in every context), see “Commas and Periods with Quotation Marks,” at CMOS Shop Talk.