The Controller class has too many responsibilities and it would be desirable to separate these responsibilities into separate classes:

1., Configuration Management (configHandler): inject the configHandler singleton whereever it is needed and try to remove/extract those parts of the code that have Feature Envy (e.g. when configHandler is used in connection with TopicMessageTypeConfig):
Map<String, TopicMessageTypeConfig> configs = configHandler.getTopicConfigForClusterIdentifier(selectedCluster().getIdentifier());
TopicMessageTypeConfig topicMessageTypeConfig = getTopicMessageTypeConfig(configs); //configHandler is also used inside this method
Map<String, String> consumerConfig = configHandler.readConsumerConfigs(selectedCluster().getIdentifier());

2., Kafka Service Layer: e.g. Number of Runnables executed by runInDaemonThread need only singletons like consumerHandlers injected, but probably do not need to be part of the JavaFx Controller

3., EventHandlers passed as parameter in setOnAction can be very likely extracted. Be aware that these EventHandlers will also benefit from 1., and 2.,

I will give prio high to this issue, since it can dramatically increase the speed of future develepmoent tasks.