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This paper explores the use of Autoencoder (AE) models to identify Koopman-based linear representations for designing model predictive control (MPC) for wind farms. Wake interactions in wind farms are challenging to model, previously addressed with Koopman lifted states. In this study we investigate the performance of two AE models: The first AE model estimates the wind speeds acting on the turbines these are affected by changes in turbine control inputs. The wind speeds estimated by this AE model are then used in a second step to calculate the power output via a simple turbine model based on physical equations. The second AE model directly estimates the wind farm output, i.e., both turbine and wake dynamics are modeled. The primary inquiry of this study addresses whether any of these two AE-based models can surpass previously identified Koopman models based on physically motivated lifted states. We find that the first AE model, which estimates the wind speed and hence includes the wake dynamics, but excludes the turbine dynamics outperforms the existing physically motivated Koopman model. However, the second AE model, which estimates the farm power directly, underperforms when the turbines' underlying physical assumptions are correct. We additionally investigate specific conditions under which the second, purely data-driven AE model can excel: Notably, when modeling assumptions, such as the wind turbine power coefficient, are erroneous and remain unchecked within the MPC controller. In such cases, the data-driven AE models, when updated with recent data reflecting changed system dynamics, can outperform physicsbased models operating under outdated assumptions.