Learn English – Period with quotes and double quotes

Put the scare-quoted material in single quotes, just as you would do with any other nested quotation. It's not your responsibility to distinguish between genuine quotations and scare quotes in the source material--and if you put yourself in that position, there's a chance you could guess wrong, which could open you to charges of misquotation. (For that matter, you could be accused of misquotation for dropping quotation marks, regardless.)

The APA Style Guide is not a legal text trying to cover all bases in a final way. You are quoting the word stuff in the sense that you are putting quotation marks around it. Unless you are quoting the question Stuff?, the question mark is obviously not part of the quoted material.

Also, the APA Style Guide is only for dubious cases. Since there was never a typographic tradition of putting large punctuation such as question marks inside the quotation marks when they don't logically belong there, the question doesn't even arise for question marks in the first place and so naturally the APA Style Guide was not written with the intent of settling it. (The tradition of putting periods and commas inside the quotation marks was originally in order to put them closer to an alphabetic letter so as to protect the delicate (physical) letter/type/sort against breaking off. It is only by inertia that some style guides still require it now that the necessity no longer exists. To the extent that there is an optical problem, a thin negative space that could be applied automatically would be a better solution.) It's just an accident that the APA Style Guide can be interpreted so as to yield the correct result.