All my style guides are crated up, but I see no error or ambiguity to #1, whereas #2 is a construction that I don't recall encountering in many years of reading.

There are situations that call for punctuation outside the quotes, though those are fairly uncommon.

Here's the definitive word from the Purdue OWL:

Place a question mark or exclamation point within closing quotation marks if the punctuation applies to the quotation itself. Place the punctuation outside the closing quotation marks if the punctuation applies to the whole sentence.

Phillip asked, "Do you need this book?"

Does Dr. Lim always say to her students, "You must work harder"?