Yes, $|\psi(t)|^2$ is an instantaneous probability density.
Passage of a wave packet can be experimentally observed.
An isolated system can be in a superposition of different energy eigenfunctions. It does not violate the energy conservation law because initially the system is not in an eigenstate - it has some energy uncertainty at $t=0$. This uncertainty evolves as any other uncertainty.
EDIT: Let us make a superposition of two states: $$\psi(t)=c_1\psi_1(x)e^{-iE_1 t}+c_2\psi_2(x)e^{-iE_2 t}.$$ It means that we can find in experiment the system in state 1 with probability $|c_1|^2$ and in state 2 with probability $|c_2|^2$. The system is free and this is due to coefficients $c_1$ and $c_2$ being constant in time (occupation numbers do not depend on time).
Measuring the system energy will give sometimes $E_1$ and sometimes $E_2$, with the same probabilities. So initially and later on the system does not have a certain energy. The state $H\psi$ depends on time as $$H\psi=c_1 E_1 \psi_1(x)e^{-iE_1 t}+c_2 E_2 \psi_2(x)e^{-iE_2 t}.$$ It is not an eigenstate of the Hamiltonian, so the time derivative $\partial\psi/\partial t$ is not proportional to $\psi$.
The Hamiltonian expectation value, however, does not depend on time: $$\langle\psi|H|\psi\rangle = |c_1|^2 E_1 + |c_2|^2 E_2 = const.$$
In other words, it is the energy expectation value that conserves, not the energy. The latter is undefined, uncertain in this free state.
You invoke the "energy conservation law" $dH/dt=0$ which is an operator relationship. If the system has a certain energy $E_n$ in the initial state, this value remains the system energy in later moments, so your "conservation law" may be cast in a form $dE(t)/dt=0$ that means $E=const=E(0)=E_n$.
But if the system does not have a certain energy at the initial state $\psi(0)$, then there is no $E(0)$ to conserve and your operator relationship turns into conservation of the expectation value.