Once you recognize the name of the shadow property, you can use (at least in EF Core 1.1.0) the HasIndex method based on overload
public virtual IndexBuilder HasIndex(params string[] propertyNames)
eg.
entityTypeBuilder .HasIndex("Name", "CategoryId" }) .IsUnique();
Same for HasAlternateKey :
entityTypeBuilder .HasAlternateKey("Name", "CategoryId" });
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