Very interesting case study. We ran into the Fuse issue ourselves, but in our case we were able to drop back to a headless JRE install. Other than that we have run into very few major issues using Docker in our prototype production architecture. We currently have images for quickly deploying elasticsearch, our logstash logging infrastructure, and a number of custom components. The main benefits for us so far have been the improved maintainability and ease of deployment of declaratively configured images, and the strong sandboxing and dependency control.
I wonder how or if docker relates to their provisioning of containers for .net tasks.