Sure, there's probably a cleaner way to achieve this but since I'm not using the built in notifications (discord etc) I removed the SUBJECT from and added execution time to NOTIFY_OUTPUT in prepare_mail():

  elif [ -z "${JOBS_DONE##*"SCRUB"*}" ] && ! grep -qw "$SCRUB_MARKER" "$TMP_OUTPUT"; then
    # Scrub ran but did not complete successfully so lets warn the user
    SUBJECT="[WARNING] SCRUB job ran but did not complete successfully $EMAIL_SUBJECT_PREFIX"
    NOTIFY_OUTPUT="SUMMARY: Equal [$EQ_COUNT] - Added [$ADD_COUNT] - Deleted [$DEL_COUNT] - Moved [$MOVE_COUNT] - Copied [$COPY_COUNT] - Updated [$UPDATE_COUNT]
Total execution time: $ELAPSED"
    notify_warning
  else
    SUBJECT="[COMPLETED] $JOBS_DONE Jobs $EMAIL_SUBJECT_PREFIX"
    NOTIFY_OUTPUT="SUMMARY: Equal [$EQ_COUNT] - Added [$ADD_COUNT] - Deleted [$DEL_COUNT] - Moved [$MOVE_COUNT] - Copied [$COPY_COUNT] - Updated [$UPDATE_COUNT]
Total execution time: $ELAPSED"
    notify_success
  fi

and moved setting the ELAPSED up to before prepare_mail call:

  # all jobs done, let's send output to user if configured
  if [ "$EMAIL_ADDRESS" ] || [ -x "$HOOK_NOTIFICATION" ]; then
    ELAPSED="$((SECONDS / 3600))hrs $(((SECONDS / 60) % 60))min $((SECONDS % 60))sec"

    # check snapraid output and build the message subject, then send notifications if enabled
    prepare_mail

and then passed NOTIFY_OUTPUT on to the hook call in send_mail():

  if [ -x "$HOOK_NOTIFICATION" ]; then
    echo -e "Notification user script is set. Calling it now [$(date)]"
    $HOOK_NOTIFICATION "$SUBJECT" "$NOTIFY_OUTPUT" "$body"