That's true, the EmptyDefinition property is never set

private static SiteDefinition EmptyDefinition;
// ...
public static SiteDefinition Empty
{
    get
    {
        return EmptyDefinition ?? new SiteDefinition
        {
            StartPage = ContentReference.EmptyReference
        };
    }
    internal set
    {
        EmptyDefinition = value;
    }
}

This property will always be recreated.

Create a custom class if you must have a singleton :P

public class SiteDefinitionCustom : IReadOnly<SiteDefinitionCustom>, IReadOnly
{
    private static SiteDefinition EmptyDefinition;

    public bool IsReadOnly { get; private set; }

    public static SiteDefinition Empty
    {
        get
        {
            // horrible but will work 😁
            if(EmptyDefinition is null)
            {
                EmptyDefinition = new SiteDefinition
                {
                    StartPage = ContentReference.EmptyReference
                };
            }
            return EmptyDefinition; 
        }
        internal set
        {
            EmptyDefinition = value;
        }
    }

    public object CreateWritableClone()
    {
        throw new NotImplementedException();
    }

    public void MakeReadOnly()
    {
        throw new NotImplementedException();
    }

    SiteDefinitionCustom IReadOnly<SiteDefinitionCustom>.CreateWritableClone()
    {
        throw new NotImplementedException();
    }
}

Looks like a mismatch between xml doc and actual code. I will file a bug to Content platform team to correct it. thanks for bringing it to our attention