I know the mechanics behind the separation of variables and how it is used to solve PDEs; however, I am confused by the assumption behind the separation constant.
Taking the wave equation as an example: $\frac{d^2(u)}{dt^2} =c^2\frac{d^2(u)}{dx^2}$ with the separation of variables, where $u(t,x)=X(x)T(t)$ we derive the expression: $\frac{T''}{T}=c^2\frac{X''}{X}=\omega$ where $\omega$ is the separation constant.
So here, many texts and videos state that since the left hand side is a function of only time and the right hand side is a function of only space (x); therefore, the $\omega$ has to be a constant.
I am confused about $c^2$, from the derivation of the wave equation we know that $c$ represents the velocity and is not dimensionless. So why is it not taken into consideration? Have I overlooked something? Thanks in advance :)
It is not necessary to repeat the argument so that $$\frac{T''}{T}=c^2\frac{X''}{X}=\omega=\text{constant}$$ You have well set out the argument.
More generally, consider the next PDE : $$\frac{d^2(u)}{dt^2} =\left(c_1(x)c_2(y)\right)^2\frac{d^2(u)}{dx^2}$$ where $c$ is no longer a constant but the product of a function of $x$ and a function of $y$. The separation of variables leads to : $$\frac{1}{\left(c_2(y)\right)^2}\frac{T''}{T}=\left(c_1(x)\right)^2\frac{X''}{X}=\omega=\text{constant}$$ $\omega$ is any constant. There is no reason to say that a constant $\omega$ be related to a function $c_1(x)$ or to another function $c_2(y)$. So, it would be senseless to ask " Why $c_1$ or $c_2$ are not taken into consideration? ".
That is the same for the simpler case where $c_1(x)=c=$constant and $c_2(x)=1$.
In fact $c$ is effectively taken into consideration, but not at this step of calculus. It is taken into consideration at next step when the equation $c^2\frac{X''}{X}=\omega$ is solved.
For each value of $\omega$ the solutions involve $c$. They are as many solutions with $c$ into them than they are different $\omega$ and also the linear combinations of those solutions. So, they are an infinity of solutions until no boundary conditions is specified.