That's actually one of the primary use cases at the moment. The way Mutagen works with Docker is by using `docker cp` to inject one of its "agent" binaries into the container and then communicating with that binary over `docker exec`.
You can also orchestrate your setup a bit (e.g. to work with Docker Compose) using Mutagen's new orchestration infrastructure. You can find an example of this at the bottom of the Mutagen homepage: https://mutagen.io
It's designed for a different purpose - bidirectional sync. Though it does use the rsync algorithm for efficient transfers. It also does file monitoring. Closer to Unison really, though with a slightly different and more modern approach.
You can also orchestrate your setup a bit (e.g. to work with Docker Compose) using Mutagen's new orchestration infrastructure. You can find an example of this at the bottom of the Mutagen homepage: https://mutagen.io