The difference in approach is that the clone is a lower-level thing. Duplicati has to use high-level APIs which mostly prefer to do the usual magic (rather than go below it), such as downloading on file open.
Reparse Points and File Operations shows that there might be hope if direct WIN32 access was used, however Duplicati tries to stay with what .NET Framework provides, and I haven’t found that one yet…
Duplicati also uses AlphaFS which at least can return FileSystemEntryInfo.ReparsePointTag Property, however I’m not sure how you set that tag or get/set the reparse data as mentioned in Reparse Points.
I can see the reason why you’d like to not download the world, and why you’d want to backup changes existing purely locally, but I’m interested in how backing up placeholders most useful online adds value. Even if it adds value, I’m not sure if it can be done, but without value it’s probably not worth much work.
NTFS multiple data streams on alternate data streams was a similar discussion, and has similar issues.