Using the Dockerized image can be convenient as it contains, by default, all the tools you need to run your analysis: you won't need to install anything else. However, when a complex pipeline is used, in presence of a docker-in-docker setup or when specific version of the tooling is needed, you can always revert to the Java Thin client. This will require you to install all the tools you need but it will grant you greater control to the specifics of the environment, including of course specific version of tools.