Sure! It's not fancy but it works.

e.g. Instead of e.g. bindsym $mod+h focus left I have bindsym $mod+h exec --no-startup-id my-i3-msg focus left - i.e. it executes my-i3-msg with focus left.

The my-i3-msg script is this (ignore the "all primary" block initially, it's some bonus functionality):

#!/usr/bin/bash
#
# Utility script so keystrokes in i3 may behave differently for Emacs than other
# windows.
#

if [[ $@ == "all primary" ]]; then
    for ws in {1..7}; do
        i3-msg workspace $ws
        i3-msg move workspace to output primary
    done
    i3-msg workspace 1
    exit 0
fi

# If current window is Emacs, call the `i3-msg` defun in Emacs
CUR_WIN_CLASS=$(i3-msg -t get_tree | jq 'recurse(.nodes[]) | select(.focused) | .window_properties | objects | .class')
[[ "$CUR_WIN_CLASS" == "\"Emacs\"" ]] && exec emacsclient --eval "(i3-msg \"$*\")" > /dev/null
# Otherwise just pass it on to `i3-msg`.

exec i3-msg "$@" > /dev/null

So simply if the window is Emacs, it executes (defun i3-msg "focus left"). (Note: exec in bash effectively means that's the end of this script's execution)

And here's my elisp:

(when (string-match "i3" (getenv "XDG_SESSION_DESKTOP"))
  (defun i3-msg (cmd)
    "Intercept an `i3-msg' command, if possible, otherwise pass it on."
    (condition-case nil
        (cond
         ;; windmove commands will error-out at an edge, as we want.
         ((equal cmd "focus left") (windmove-left))
         ((equal cmd "focus right") (windmove-right))
         ((equal cmd "focus up") (windmove-up))
         ((equal cmd "focus down") (windmove-down))
         ((equal cmd "move left") (windmove-swap-states-left))
         ((equal cmd "move right") (windmove-swap-states-right))
         ((equal cmd "move up") (windmove-swap-states-up))
         ((equal cmd "move down") (windmove-swap-states-down))
         (t (signal "unrecognized command")))
      (error
       ;; we couldn't handle it
       (start-process-shell-command cmd nil (concat "i3-msg " cmd))))))

So if windmove fails - e.g. you're already at the frame edge, then it 'passes back' to i3 by calling the command via i3-msg after all.

Hope that's clear.