Why do we only consider relative motion of hydrogenic atoms?
We can do that because the variables have separated. The Hamiltonian of relative motion depends on the relative coordinates. The translational part depends on the coordinates of the center of mass. The two never mix. They don't interact; they don't even care about each other.

Separation of variables in various guises is an immensely powerful technique of solving PDE. You will encounter it time and again, including this very chapter of whatever textbook you are using, just a few lines below, when you'll start to actually solve the equation for hydrogen atom by splitting it into radial and angular parts.

So it goes.