Safe-js also exposes the low-level-api and as said before, we are intending on keeping most things backwards compatible in that area, too.
The low level API gives you more direct access to the network and its resources and it is available for desktop as well as a web apps.
In particular this allows you to have much more fine grained control which kind of Data-Type certain things are stored in - ImmutableData, StructuredData or AppendableData. Thus for example what we are doing in the comments-tutorial requires features of the AppendableData that you can't access with the NFS emulation, therefore it needs access to the Low-Level-API.
As mentioned in the Auth-RFC, we are intending on merging more of those features directly into the API and offer emulations like NFS on top for convenience, but with handing out App-Keys in the future, there is no preventing anyone from doing low-level-operations anymore anyways, so we decided to embrace it instead.