In general, a surface integral is exactly the same as an area integral, the only key difference is that it measures the surface area of a non flat surface.
For the same boundary, $\iint da$ will have a different value for every singe surface attached to that closed boundary, because the surface area of a surface depends upon the surface.
Now we have faradays law, which instead of a surface integral, it is a weighted sum of $\frac{\partial \vec{B}} {\partial t} \cdot \vec{da}$. This isn't just a measure of surface area, it is a measure of how much the time derivative of the magnetic field points directly into a chosen surface, * area.
There is a major difference between a regular surface integral and faradays law.
$\oint \vec{E} \cdot \vec{dl} = -\iint \frac{\partial \vec{B}} {\partial t} \cdot \vec{da}$
Here we have a line integral that only depends on the BOUNDARY, equated to a surface integral that shares a boundary with the line integral. This surface integral IS INDEPENDANT of the surface chosen, and unlike the regular surface integral, it only depends upon the boundary, not the surface.
Why is there a difference?
The key in understanding this is that for the integral to be independant of the surface, the inside function must have zero divergence.
Mathematically, we can easily prove this by assuming that this is true for all surfaces, and then finding the condition on B upon which this statement is true, and showing that it is indeed true.
$\oint \vec{E} \cdot \vec{dl} = -\iint\frac{\partial \vec{B}} {\partial t} \cdot \vec{da}$
$\iint \nabla × \vec{E} \cdot \vec{da} = -\iint\frac{\partial \vec{B}} {\partial t} \cdot \vec{da}$
The fact that I cross the surface off here indicates that I'm saying it is true for any surface attached to $\vec{dl}$
$ \nabla × \vec{E} = -\frac{\partial \vec{B}} {\partial t} $
Taking the divergence of both sides
$0 = \nabla \cdot \frac{\partial \vec{B}} {\partial t} $
$\nabla \cdot \vec{B} = c$
Meaning the condition upon which this is true for any surface is when the divergence of $\vec{B}$ is a constant, which is inline with the condition that $\nabla \cdot \vec{B} = 0$
The intuitive way of showing this, is that for the surface integral to be independant of the surface, the fluxes of 2 chosen surfaces of the same boundary must be the same, meaning constructing a closed surface out of those 2 surfaces, would change $\vec{da}$ for one of them, meaning the total flux out of the closed surface will be $\phi +(-\phi)$ = 0, using divergence theorem we see that this must be 0.