I'm not sure if this is the correct way to solve it, or this should be the 'answer' but I managed to get my robot footprint to change dynamically via C++ by using dynamic_reconfigure dynparam, like this:

 std::string footprint_str = "[[0.83,-0.28],[0.356,-0.28],[0.166,-0.3],[-0.03,-0.3],[-0.03,0.3],[0.166,0.3],[0.356,0.28],[0.83,0.28]]";
 std::string footprint_node = "rosrun dynamic_reconfigure dynparam set /move_base/local_costmap footprint ";
 system((footprint_node + footprint_str).c_str());

This came from here UsingDynparamToChangeHokuyoLaserParameters (at the bottom of the page)

So when you change footprint_str (which I'm doing manually at the moment via a lookup table of sorts) the actual robot footprint changes to match it straightaway.

I would like to use something like this example but this code doesn't look complete and I don't know enough about point32 arrays, tf2::doTransform and then how to get this back to a string.

Long story short, it works good enough for me. Although now when I kill the node it says escalating to SIGTERM, probably due to the 'system' call, it'll work until a proper solution comes around. anyone??? ;)

#!/usr/bin/python3
import rospy
from std_msgs.msg import Float32
import dynamic_reconfigure.client

rospy.wait_for_service('/move_base/local_costmap/set_parameters')
client = dynamic_reconfigure.client.Client("/move_base/local_costmap", timeout=2, config_callback=None)

def callback(data):
    footprint_str="points in here"
    client.update_configuration({"footprint":footprint_str})

def listener():
    rospy.init_node('dyn_fp')#, anonymous=True)
    rospy.spin()

if __name__ == '__main_
    listener()

Inspired from Zonared's answer this is what I use:

import rospy
from dynamic_reconfigure.client import Client
from rospy.exceptions import ROSException
import time

def set_footprint(footprint):
    rospy.init_node("footprint_updater")

    new_config = {"footprint": footprint}

    service_wait_timeout = 2 # seconds
    num_trials = 5
    trial_intervals = 0.5 # seconds

    # Create a client for the global costmap
    try:
        rospy.wait_for_service("/move_base/global_costmap/set_parameters", timeout=service_wait_timeout)
        global_client = Client("/move_base/global_costmap")
        global_client.update_configuration(new_config)

        updated = False
        for _ in range(num_trials):
            time.sleep(trial_intervals)  # wait for the parameter to be updated
            updated_footprint = rospy.get_param("/move_base/global_costmap/footprint")
            if updated_footprint == str(footprint):
                updated = True
                break
        if not updated:
            rospy.logerr("Failed to update global costmap footprint.")
    except (ROSException, Exception) as e:
        rospy.logerr("Failed to create a client for global costmap or update its footprint: {}".format(e))

    # Create a client for the local costmap
    try:
        rospy.wait_for_service("/move_base/local_costmap/set_parameters", timeout=service_wait_timeout)
        local_client = Client("/move_base/local_costmap")
        local_client.update_configuration(new_config)

        updated = False
        for _ in range(num_trials):
            time.sleep(trial_intervals)  # wait for the parameter to be updated
            updated_footprint = rospy.get_param("/move_base/local_costmap/footprint")
            if updated_footprint == str(footprint):
                updated = True
                break
        if not updated:
            rospy.logerr("Failed to update local costmap footprint.")
    except (ROSException, Exception) as e:
        rospy.logerr("Failed to create a client for local costmap or update its footprint: {}".format(e))

def main():
    # Example polygon
    # footprint = [[1.0,-1.0], [1.0,1.0], [-1.0,1.0], [-1.0,-1.0]]
    footprint = [[0.5, 0.5], [0.5, -0.5], [-0.5, -0.5], [-0.5, 0.5]]
    set_footprint(footprint)

if __name__ == "__main__":
    main()