Newton's second law $F=ma$ does not depend on the point of application of force because this law is valid only for point particles. Now to apply it to rigid bodies we must consider them as a system of particles.
Let a rigid body be made up of $N$ particles of mass $m_1,m_2,\cdots,m_N$. Now apply a force $f$ to some $i_{th}$ particle. All other particles will also exert internal forces on each other.
Therefore, the second law for all particles is
\begin{align}f_1^{int}&=\frac{dp_1}{dt}\\
f_2^{int}&=\frac{dp_2}{dt}\\
\cdots\\
f+f_i^{int}&=\frac{dp_i}{dt}\\
\cdots\\
f_N^{int}&=\frac{dp_N}{dt}\end{align}
Adding all these
$$\sum_j f_j^{int}+f=\sum_j\frac{dp_j}{dt}$$
By the third law
$$\sum_j f_j^{int}=0$$
Thus
$$f=\frac{dP}{dt} \text{where } P=\sum_jp_j$$
Now if you apply the same force $f$ to the center of mass of the body, you get the same equation for total momentum.
$$f=\frac{dP}{dt}$$
Therefore both situations will have identical solution for the total momentum and hence for the linear velocity of the center of mass of the rigid body.