Here is an updated version of that tutorial,
https://docs.quantumwise.com/tutorials/phonon_calcs/phonon_calcs.html.
For calculating the transmission spectrum of the 3D conductor, the k-point sampling for the 2D Brillouin zone corresponding to the lateral unit cell should be chosen such that the transmission is converged with respect to the number of k-points. But if you calculate the transmission spectrum for a quasi-1D system, you may then just use a single Gamma k-point.