Workaround (copied from my own post here:
http://superuser.com/a/1003494/261244):

An xinput set-button-map alternative can be used, but is less dynamic
(it will not be applied automatically when your device is detected). The
following script can be configured to run at startup (in Ubuntu there is
a Startup Applications GUI to set it up). For some reasons it won't work
if you simply call the script from your ~/.profile file. The MOUSE_NAME
variable corresponds to whatever name is given to your mouse in the
output of the xinput list command.

#!/bin/bash

MOUSE_NAME="Razer Razer Lachesis"
BUTTONS_MAP="3 2 1"

while read -r line; do
    raw_line=$(grep "$MOUSE_NAME" | grep "pointer")
    if [ ! -z "$raw_line" ]; then
        mouse_id=$(echo "$raw_line" | cut -d '=' -f2 | sed 's/\t.*//g')
        echo "Found ${MOUSE_NAME}'s id: $mouse_id"
        xinput set-button-map $mouse_id $BUTTONS_MAP
        break
    fi
done < <(xinput list)

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https://bugs.launchpad.net/bugs/1518653

Title:
  Custom xorg input device configurations are not honored

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