Many 'proofs' of Faraday's law use the third of the Maxwell's equations $\nabla \times \bf {E} = -\dfrac {\partial B}{\partial \it t}$ to simplify the flux integral by first splitting it into two integrals. One for the time-dependent magnetic field and one for the change in flux when the surface is time dependent.
$$\dfrac {d\phi_{B}}{dt} \Bigg|_{t=t_{0}}= \int \int_{\Sigma (t_{0})} \dfrac {\partial \textbf {B}}{\partial t} \Bigg |_{t = t_{0}} \cdot d \textbf {a} + \dfrac {d}{dt} \int \int_{\Sigma(t)} \textbf B( t_{0}) \cdot d \bf a $$
Why is the second of these integrals even needed? $\nabla \cdot \bf B$ $ = 0$ so from vector calculus we already know that the flux across surfaces with the same boundary curve $\partial \Sigma$ is the same...
This also doesn't make sense intuitively - $\Sigma$ is not a physical surface so the flux should't depend on it's actual shape but only it's boundary (i.e. the (physical) conducting loop). I get the derivations but can't see why the SHAPE of the surface should effect the flux. So what's going on here? Or is the divergence of time-dependent magnetic fields not zero in some cases?