The Chicago manual (14th ed.) provides this guidance in sections 5.134-5:
The use of more than one mark of punctuation at the same location in a sentence (multiple punctuation) is, for the most part, limited to instances involving quotation marks, parentheses, brackets, or dashes. An abbreviating period, however, is never omitted before a mark of sentence punctuation unless the latter is the period terminating a sentence.
When more than one mark of punctuation (excepting quotation marks, parentheses, brackets, and sometimes dashes) is called for at one location in a sentence, only the stronger or more necessary mark is retained.
Despite the fact that Chicago does not provide a specific comment on the question mark, when I look at the language of their comment closely, it does appear to me to clearly advise the retention of abbreviating periods in the case of terminating question marks, which are clearly not periods.
Thus, the following is correct:
What has been done for instances of X, including 1, 2, 3, etc.?
Have you taken care of all you are required to do, like A, B, C, etc.?
Does Thomas really have a Ph.D.?
(Note: I was half expecting the commentary on question marks (5.133) to state that question marks should be treated like periods when terminating a sentence, but this comment is NOT made. Rather, they subordinate the discussion of question marks to the localized discussions of other punctuation marks. Thus, it should be perfectly clear that the omission of question marks in the statement "unless the later is the period terminating a sentence" does carry the weight of an explicit exclusion of question marks.)
The Chicago manual does support the use of a combined "?!", and provides this example (among others), the order of which I have slightly modified so as to make it read like a narrative, plus I have added an ending:
Go home.
Go home?
Go home!
Go home?!
[Yes! Go! Home!]
The doubling of punctuation for emphasis in formal writing is universally frowned upon. It is, however, common in informal writing.