ZFS dedup is memory constrained, and the memory use scales with the block hashes.

If performance isn’t a concern, you’re better off compressing your media. You’ll get similar storage efficiency with less crash consistency risk.

The pro/con has more to do with how you want to run your system and manage changes.

Containerization is primarily about repeatability and declarative configuration management. If you want to repeat the same configuration with every deployment and/or upgrade, containers are the way to go.

If you want to tweak and manage the software the way you want it and aren’t concerned with configuration drift, then install it as a service.