in LTE-A uplink, the effective channel matrix (including the precoder) from each transmission layer to each receive antenna is estimated. In case spatial correlation is ignored, this is done for each of these channels separately. Further, channel estimation in LTE is pilod aided. The channel matrix is estimated only on pilot positions and then interpolated between those pilot positions. See
for more information.
Of course, the channel for each user is different and each user has its own channel matrix. So in this sense, no, the channel matrix size does not change with the number of users.
In our link level simulator, there is no cell geometry implemented. There exists no cell size, no distance and no path loss. Channels are generated according to a tap-delay model for the power delay profile plus a Jakes model for time selectivity. Therefore, there also exists no scenario definition like macro or micro cell in the link level simulator. This would be a topic for system level simulation.