I have never used it, but as I understand it, the HiFiHaven ripping process is just a packaged version of the Computer Audiophile process that uses the Sonore ISO2DSD program to split the ISO into multiple tracks. It produces metadata from the original SACD.
It seems like there are a couple of problems here.
As to MC looking up the "correct" metadata, that can be hard to do if the basic metadata like [Album] and [Album Artist] that MC uses to identify an album are the same for the CD and the SACD rip. Discogs uses barcodes since those are unique. Using just a few metadata values unfortunately cannot guarantee a unique identification of a SACD versus a CD. Sometimes there may be enough metadata to make the unique identification and sometimes not. Given the nature of the MC metadata database, it will not always identify the correct album.
The problem with your dsf files being mixed with the CD files is that if the metadata from your process produces metadata that is the same as for the CD for the fields that MC uses to organize albums , it will mix the tracks. If your files have the same [Album] and [AlbumArtist (auto)] as the CD tracks, then MC may see them as the same album and mix them together. In that case, you need to either rename something, like adding SACD to the album name. That will separate the albums. You can also define you view scheme to separate different file types, but that is trickier to do.
As you found, mixing SACD and CD albums is tricky given they way MC identifies album. Unfortunately, it is often a somewhat manual process.
