The manual on TransmissionEigenstate does not say that "the transmission eigenstates are linear combinations of Bloch states of the electrodes".
In the manual section you refer to, it is said that "t_{nk} is the transmission amplitude from Bloch state \psi_n in the left electrode to Bloch state \psi_k in the right electrode.
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The transmission eigenstates are obtained by propagating the linear combination of the Bloch states".
It means that the transmission eigenstates are the linear combination of the Bloch states in the semi-infinite electrodes, not the central region. The corresponding electron wave function given by this linear combination of the Bloch states is then effectively matched to the electron wave function in the central region by propagation through the central region.
A good textbook example is the electron scattering on a square barrier potential, where the wave function in the electrodes is a linear combination of an incoming and reflected Bloch state of the electron, which are just two plane waves in this case indeed. The under barrier wave function is a simple decaying function that has to be matched to the wave function in the electrodes.
You may solve the same problem without explicit wave-function matching, e.g., by propagation of the corresponding states of the electrodes through the central region. And this is what is described in Jeremy's thesis as well as in most dissertations on quantum transport.