I would consider the second sentence borderline unacceptable, the direct address masking the comma splice. Better would be
Don't touch that, John. It'll explode.
The first comma is necessary in direct address. Although it gets left out in emails and texts and chat quite often, in more formal writing you would always use it:
Hello, Mary.
How are you, Mark?
What's up, Doc?
Did you find your slippers, dear?
Finally,
Don't touch that John.
would seem to be cautioning people not to touch a certain individual named John.
The three reference guidelines that you quote in your question evidently apply to any "parenthetical element," "introductory word, phrase, or clause," or "parenthetical or unnecessary expression" that immediately follows a coordinating conjunction—and the direct-address word "John" in your example is simply one such element, word, or expression.
That being the case, it seems to me that all three sources you cite would endorse omitting a comma immediately after the conjunction, yielding these sentences:
I was going to accept your resignation later, but John, have you considered all the options first?
I will be flying with the executive committee to London, and John, will you be coming with us?
The only asterisk attached to this endorsement is that Science and Technical Writing: A Manual of Style also approves of the alternative punctuation with a comma after the coordinating conjunction:
I was going to accept your resignation later, but, John, have you considered all the options first?
I will be flying with the executive committee to London, and, John, will you be coming with us?
So if you're following Dr. Darling or Morson, you should omit the comma after and or but; and if you're following Science & Technical Writing, you can choose either to omit the comma or to include it. I should note, however, that these three sources do not speak for more than themselves: there is no universally recognized rule of punctuation on this point.
Having said all that, I must reiterate Edwin Ashworth's suggestion that either preceding the conjunction with a semicolon or breaking the compound sentence into two sentences would do more to clarify the sense of the sentence on first reading than simply adopting one or the other approach to the comma question. Alternatively, in the first example, shifting "John" to a position immediately before the conjunction instead of immediately after it would enable you to punctuate the interior of the compound sentence entirely with commas, without fogging up the construction:
I was going to accept your resignation later, John, but have you considered all the options first?
In the second example, merely relocating "John" is less satisfactory because the choice of and as the coordinating conjunction becomes less appealing when "John" moves elsewhere. In that case, I would consider introducing an em-dash to indicate a redirection of thought midway through the compound sentence:
I will be flying with the executive committee to London—and will you be coming with us, John?
Best Answer
I don't know about the vocative aspect but the Chicago Manual of Style advises that a “direct address” should be set off by commas. A direct address occurs when you call someone by a name or other term used like a name. So in your example, "Hello, world," that comma is correct. However, I frequently see the comma being dropped in everyday communication.