I'm by no means an expert on copyright law or copy protection, but I think that using any method other than writing directly to the MBR with those copy protection measures would be illegal because writing to a file (registry, wine-only proprietary db or any other type of file) as opposed to writing to the mbr like the copy protection is supposed to could potentially reveal data that the copy protection companies don't want being revealed, and therefore that would end up making wine a possible target for aiding circumvention. Sure there are tools out there that crackers use that read the mbr and store it in a file, so that they can circumvent the copy protection, but that has nothing to do with wine.
Could you not say the same thing for vmware or any other virtual harddrive application?