A DDS person would tell you to use partitions, probably. For us, since we're currently using DDS partitions in our implementation and don't expose them through the ROS 2 api, I would advise you to just use ROS namespaces. We're planning on having more sophisticated at runtime and during runtime topic manipulation to help with this.
I gained a lot of insight on what would be needed to deal with situations like this when working on the [capabilities](
https://github.com/osrf/capabilities) package as part of the rocon project. I think with some more options to configure the namespaces (remapping and aliasing) it will be a more tractable problem, but we don't have those features yet.
A stronger separation would be to have different domains and have some bridges to expose parts of one domain to another.
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