Actually SeaweedFS does just that, append small objects into larger blocks during write or update, and run garbage collection during compaction.
I think the document should have a clearer guideline about best practices when deploying a SeaweedFS cluster for different situations: small cluster, large cluster, H/A cluster etc..
For filer metadata, you should just pick the one you are most familiar with.
There is a wiki page for production setup. https://github.com/chrislusf/seaweedfs/wiki/Production-Setup