In the documentation for the costmap_2d they mention that there is a subscription to the footprint topic. This led me to believe that you ought to be able to publish on one of the <costmap>/footprint and have everything be automatically updated. A quick test shows that this does appear to be the case (although I haven't thoroughly tested). In the source code you can see they do indeed subscribe to the topic, and that the subscribed footprint eventually changes the local attribute, and further, this eventually is published back to the topic.