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In order to understand your custom message type, gztopic and the Gazebo gui would need to be recompiled and linked with the protobuf headers from your custom message type. You can write your own tools the publish and subscribe to custom messages (see the tutorial), but the pre-compiled Gazebo tools won't be able to parse them.

Unless, of coure, you did something fancy with self-describing messages, but that's probably a lot of effort.