You don't manipulate the reference directly (i.e. you shouldn't learn its numeric value (though you can - useful for debugging), and you can't change it) - but you do use it indirectly all the times with ==, eq, or however the referential equality operator is called in a given programming language.

This is what, given (excuse the Java):

    MyObject a = new String("choo choo");
    MyObject b = a;
    MyObject c = new String("choo choo");

allows you to observe that:

    a == b;
    a != c;
    b != c;

even though:

    a.equals(b);
    a.equals(c);
    b.equals(c);

under string comparison.

This is exactly like surrogate keys. An implementation detail that's crucial to the meaning of the whole thing.