First, note that "perpendicular to a differential area $dA$" limits the direction to two directions: "in" and "out." This should be obvious for a flat surface, but is also true for curved surfaces. In that case, imagine a flat plane tangent to the surface at a given point; that will limit the direction of $d\vec{A}$ to two directions at that point (the direction of $d\vec{A}$ will vary with position on your surface).
Second, note that reversing the direction of $d\vec{A}$ will change the algebraic sign of $\Phi_B$. This is okay, because you're not directly measuring the flux; you're measuring the eletcric and magnetic fields, the currents, and the voltages. What is physical about the magnetic flux and Faraday's law of induction is the magnitude and direction of the induced voltage. The convention about the direction doesn't affect the magnitude; it only affects the direction. The direction of the induced voltage in Faraday's law is given by Lenz's law; it is the negative sign in the mathematical form of Faraday's law. This is an expression of the conservation of energy. As long as the direction that you use to calculate the magnetic flux is consistent with the direction you choose when you use Faraday's law.
But, in order to apply Faraday's law, you need a current. That current will define a direction. So for physicists, it's conventional to use the direction of the current to define which direction is "out" of the surface. The right hand rule convention in this case has you curl your fingers in the direction of the current around the surface. Your thumb points "out" of the surface. In this manner, the direction of the path around the edge of the surface determines which direction is "into" the surface and which direction is "out of" the surface.
Mathematicians still use the same right hand rule to relate the direction around the edge of the surface with the direction "into" and "out of" the surface, but there is not an inherent reason to pick one or the other direction for the path around the edge of the surface.