The strong law of action and reaction says that the forces that two bodies exert on each other have the same magnitude, opposite direction and act along the line joining the particles. When you want that last bit to be true and you want to write the force on particle $i$ as $-\nabla_i V_{ij}$, then the potential has to be a function of the relative distance.
You can see this the following way:
Take a simple potential depending on the relative distance like
$$V_{12}=|\vec r_1 - \vec r_2|$$
and compute $\vec F_1= -\nabla_1 V_{12}$. You should get $$\vec F_{12} = -|\vec r_1 - \vec r_2|^2 (\vec r_1 - \vec r_2) $$ and $\vec F_{21}=-\vec F_{12}$.
Now do the same with a potential depending on the relative velocities:
$$\hat V_{12}=|\vec v_1 - \vec v_2|$$
Somewhere you should get expressions like $\frac{\partial}{\partial x_1}v_{x1}$ but we will set them all to 1, so you get as an answer
$$\vec F_{12} = -|\vec v_1 - \vec v_2|^2 (\vec v_1 - \vec v_2) $$ and $\vec F_{21}=-\vec F_{12}$ again.
Now you might ask "the forces have same magnitude and opposite direction, shouldn't the strong law of action and reaction hold as well?"
The answer is no because of the "last bit" I mentioned above: since $\vec v_1 - \vec v_2$ is not $\vec r_1 - \vec r_2$, the force from the potential $\hat V$ doesn't point along the line joining the particles. Just think of two particles, one at x=-1 and the second at x=1, both flying in the y-direction: while $\vec r_1 - \vec r_2$ points from particle one to the other, $\vec v_1 - \vec v_2$ and the force calculated from it is zero.
This is why the strong law of action and reaction leads to the internal energy only depending on relative distances: only forces which arise from a potential depending on the relative distances point along the line joining the particles.