Actually Sigil's AddCover routine does invoke the OPF SetResourceAsCoverImage routine that sets the metadata properly. It has long done that (literally for years!). So perhaps you are not properly saving the epub afterwards? Or maybe you did not refresh the opf tab if it was open when you made the change? Try adding the cover, saving the epub and then unzipping it manually to verify that the opf has in fact been updated (both the guide and the metadata) for epub2.
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