A. Neumaier said:
The total energy is not an average over many microscopic degrees of freedom, neither is the total mass.
Even for position, which may be viewed as such an average, the microscopic degrees of freedom are never measured, so Born's rule (which is exclusively about measurement results) cannot apply even in principle!
It's really very difficult to discuss, if you don't want to understand each other. Born's rule for me applies to both pure and mixed states. For a macroscopic system, of course, we don't measure microscopic degrees of freedom (e.g., the position of all particles within the system), because we are not able to get this information, because it's too complex (if you have 1 mol of a gas, you cannot measure ##3N_{\text{A}}## position components, because it's too much information to store). What you can, however measure is the center of mass, and it's described by the operator
$$\hat{\vec{R}}=\frac{1}{M} \sum_{j} m_j \hat{\vec{x}}_j.$$
You also cannot know the mircoscopic pure state of the system but guess only a statistical operator, given the information about the system (e.g., the total energy, momentum, angular momentum of the system) and then use the maximum-entropy principle, which you may take as a fundamental principle of statistical physics (a very reasonable one, given the meaning of entropy in the information-theoretical approach). You are let to the (generalized) equilibrium distribution (most simply stated in the grand-canonical approach, where only the averages are specified),
$$\hat{\rho}=\frac{1}{Z} \exp[-\beta (\hat{H}-\vec{v} \cdot \hat{\vec{P}})],$$
here for simplicity assuming a non-rotating system, i.e., with total angular momentum 0. Then it's easy to see that all the macroscopic properties, defined by the expectation value are as expected (e.g., you have ##\hat{\vec{P}}=M \dot{\hat{\vec{X}}}## in the Heisenberg picture, which is most convenient for this discussion and thus ##\langle \vec{X} \rangle=\langle \vec{X} \rangle_{0}+\vec{v} t##). Then, if the system is very large, also the standard deviations of the macroscopic variables are small compared their values and the relevant accuracy with which these macroscopic observables are measured, so that you get classical behavior, and the fluctuations are hard to observe (although it's of course possible, and it lead to Einstein's work on Brownian motion and related subjects, finally proving the existence of atoms, molecules, etc.).
If you know more about the system than the mere values of the additive conserved quantities, you can refine your state by working in the corresponding constraints in the maximum-entropy principle, which leads to off-equibrium statistical mechanics. As with any situation, where the full information about the system (e.g., by preparing a a state for which one complete set of compatible observable take given values, which leads to a pure state described by the then uniquely defined common eigenvector of the corresponding operators), you can only make educated guesses about the right statistical description, and the maximum-entropy principle is one way to make such an educated guess. Whether or not this guess leads to a good description of the situation considered is subject to empirical confirmation and may lead to refinements of the description. This is not specific for quantum theory but for any statistical approach to a coarse-grained description, which always needs the specification of the relevant observables and the accuracy with which their determination is necessary for the corresponding "macroscopic" description.