We establish a representation of the heat flow with Wentzell boundary conditions on smooth domains as gradient descent dynamics for the entropy in a suitably extended Otto manifold of probability measures with additional boundary parts. Yet it is shown that for weak boundary diffusion, the associated Fokker-Planck dynamics cannot be recovered from any entropy-driven metric JKO-Wasserstein scheme, at least if the underlying point metric satisfies certain natural regularity assumptions. This discrepancy is illustrated in competing large-deviation heuristics in the Sanov and Schilder regimes.