To me the doi endpoint filter seems to be redundant.
Why not use this filter to retrieve a particular DOI anywhere in the metadata e.g. in references of other works so we can resolve the cited-by DOIs from the REST API?
You can use both in the same way yes, but the /works/{doi} returns just one DOI but you can use multiple filters for the DOIs albeit not the most efficient way to return DOI metadata.
We are working on a new matching API which will help with the things you have mentioned. We will probably be releasing more information on these in the coming year, be sure to follow our blog for more updates: Blog - Crossref