Question is essentially: How can the states on a quantum dot be bound when we can tunnel onto them? If plane wave states can tunnel onto them, these plane waves states and the 'bound' states will have the same energy. Thus we could find a state containing plane waves on either side of the dot and the 'bound' state. So this overall will not be a bound state. So how can we speak of an integer number of electrons on the dot?
Consider two fermi liquid reservoirs on either side of a quantum dot. When making the Coulomb blockade argument one simply says that, if there are already N electrons on the dot, the $(N+1)^{th}$, electron needs $E_{N+1}-E_{N}+\frac{e^2}{C}$ more energy to be added than the $N^{th}$ electron did. Or rather, this is the amount the chemical potential of the dot jumps once the $Nth$ electron is added. $C$ is some capacitance and this term is related simply to the electrostatic energy of the confined electrons on dot. $E_N$ is the energy of the $N^{th}$ energy level. It may be equal to $E_{N+1}$ depending on spin degeneracy and whether $N$ is odd or even. So, when we then use a gate voltage to effectively lower the energy levels of the dot, the new chemical potential of the dot will eventually align with the reservoirs' chemical potential and if a small bias is applied electrons can hop across between the reservoirs leading to a current.
However, let's step back and consider some simple tunneling transport. Consider a 1d system, where we have free space on the left and right of a generic barrier. One approach is simply to solve the Schrödinger equation. Here we find eigenstates and once this is done, if these states are not bound states, we can straightforwardly read off transmission and reflection coefficients. All of the states which represent an incident electron being reflected and transmitted are not bound states. Furthermore, all bound states have energies less than those of the states which are not bound. This is obvious as the wavevector of a bound state, in free space on either side of the barrier, must be imaginary, so its energy is less than the not bound states, for which this is not true. So, the bound states are not involved in transmission of an electron. It does make sense to consider an incident, plane wave, electron tunneling into one of these bound states; the two states have different energies.
However, this seems to be exactly what we do with the quantum dot. It seems that we do discuss tunneling into quantum dot bound states. But these states cannot be bound, as there exist plane waves in the reservoirs tunneling into them, which thus must be of same energy.
My question is this: How can the states on the dot be bound if we can tunnel onto them. As then the states have same energy as plane waves in the reservoirs and we would form non bound states. And how can we speak of an integer number of electrons on a dot if these states aren't bound?
We haven't included the fact that there is electrostatic energy. But I still don't quite see how this can help us. We simply shift the energy levels up due to this energy and still our states on the dot won't be bound if we can tunnel onto them.