These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
The message of the story is how we look at people as mirrors rather than windows.
Q could be read as a romantic adventurer or an obsessed tragic figure. Q even claims that Captain Ahab is the hero of Moby Dick. (That said, he outright admits he never actually read the book and just wanted to get his final paper done, so he probably went off the website summary and wrote from there; a time-honored tradition among people who leave things until the last minute.)
Actually, the Aesop is more along the lines of people needing to learn to think of others complexly, not that we can't understand each other.
It could even be argued that realizing that you can never understand anyone completely isn't that unfriendly an aesop, given that it allows you to begin to think of people complexly.
What Could Have Been: In the first draft, Q and the crew finally catches up to Margo in Kashmir (yes, that war-torn region in Asia), whereupon Margo dies in a freak earthquake. Considered he did the same thing for the ending of The Fault in Our Stars, Going completely off the chain in the first draft may be simply part of the regular writing process for John Green.