> We can't simply serialize/desterialize alists in key order
> because the order is reversed in Emacs. (In Emacs alists,
> if there are duplicates, the first one wins,
> in JSON the last one wins.)
  ^^^^^^^^^^^^^^^^^^^^^^^^^

If you're talking about JSON objects then no, no particular
meaning or behavior is defined for duplicate fields (keys)
in a JSON object.

A given application that handles JSON object is free to
act as you say.  And it is free to act otherwise.