What punctuation to use when quotation ends in a question mark?
I think the punctuation should be as in the last example you used where both the question mark and comma appear within the quotes:
In "Can Pigs Fly?," Bacon states.
For the question mark appearing within the quotations, The Blue Book of Grammar and Puncutation notes:
The placement of question marks with quotation marks follows logic. If a question is within the quote material, a question mark should be placed side the quotation marks.
And A Commonsense Guide to Grammar and Usage notes:
The following tip will help you decide where to put question marks and exclamation points used with quotations.
UNQUOTE TIP Take whatever is inside the quotation marks out of the sentence and out of the quotation marks. Now, how would you punctuate this new sentence? If you would use a question mark or an exclamation point, then this same punctuation belongs inside the closing mark in the original sentence.
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Correct Errors in Using Quotation Marks with Other Punctuaton
Place periods and commas inside quotation marks.
Place semicolons and colons outside quotation marks.
Update: I often rely on the Grammar Girl for answers to such questions. She has an article Combining Quotation Marks, Question Marks, AND Commas (Whew!) which cites The Chicago Manual of Style:
The Chicago Manual of Style editors make a similar recommendation for attributions, but take a new stance on titles in their newest edition (16th edition, section 6.119): they recommend keeping the comma when a title ends with a question mark or exclamation point, as in the example above from the Grammar Girl podcast. Therefore, according to Chicago, which addresses the question most directly, the best way to write the sentence is as follows:
The Christmas carol we're going to tackle today is "What Child Is This?," written in 1865 by William Chatterton Dix.
This is only my personal opinion so I (BrE) would have put it as a comment if my phone app was behaving:
In "Can Pigs Fly?", Bacon states...