I'm not sure you're going to find an authoritative answer for this question. And I'd assume that it boils down to a matter of style (preference) rather than constraints. You could use bullet points, but perhaps you'd prefer a more flowing style. Personally. I'd choose your first version, with an 'or' after the second semicolon. I prefer the 'outside-the-quote' sectioning punctuation, though I'd not worry about using !"; or ?"; (or even .";) if necessary. I doubt you'll find an endorsement closer than the following (listed sentences but not quoted sentences) from uno.edu/lrc/writingcenter which recommends:
Semicolons are generally used for lists of sentences. Although some
grammar handbooks agree that short sentences that all follow the same
grammatical pattern
(I came, I saw, I conquered)
can be separated by
commas, it is safer to use semicolons:
Francis Wayland Thurston was appalled at the statue he found: it was a
dragon; it was an octopus; it was a monster.
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
The latter example is a correct use of a comma. You are delineating the introductory part of the sentence and pointing it toward the subject "you," who needs to get a sponge first.
While it is generally acceptable to drop commas from short sentences of about 10 words or fewer, I would recommend keeping the comma in formal / technical writing.
You can also think about it like this: when speaking the sentence aloud, you naturally create a small pause between car and you. That's a clue that you may need a comma.