In General Relativity spacetime is a four dimensional Lorentzian manifold $M$ with metric tensor $g$. Being a smooth manifold, we can use coordinate systems on spacetime.
And in reality, most traditional GR exposures rely heavily on coordinate systems, so that everything is written in a specific coordinate system $(x^0,x^1,x^2,x^3)$ always. This is so common that one usually referes to the metric tensor just as $g_{\mu\nu}$, that is, by its components in a particular chart.
The trouble is that we don't know what $M$ is! I mean, we don't know at first what manifold spacetime is. This brings a problem: how does one define coordinate systems in the first place if one doesn't know spacetime fully?
A coordinate system is a chart $(U,x)$ on the open set $U\subset M$, being $x : U\to \mathbb{R}^4$ a homeomorphism. How can one build such a coordinate system if one doesn't know what actually is $M$?
I'll give just a simple example. The Schwarzschild metric is usually written as:
$$ds^2=-\left(1-\dfrac{2GM}{r}\right)dt^2+\left(1-\dfrac{2GM}{r}\right)^{-1}dr^2+r^2d\theta^2+r^2\sin^2\theta d\phi^2.$$
Since we don't know what manifold is spacetime, how can we make sense of the coordinate functions $t,r,\theta,\phi : M\to \mathbb{R}$?
This resembles spherical coordinates, but this isn't $\mathbb{R}^3\times \mathbb{R}$ after all!
So on the one hand it seems hard to define coordinate systems because we don't know what manifold is spacetime.
On the other hand, given one observer $\gamma : I\subset \mathbb{R}\to M$, we always have one coordinate system adapted to $\gamma$. In the same way, given a reference frame $e_\mu : M\to TM$ we can also construct a coordinate system adapted to it if I'm not wrong.
So since we don't know what manifold spacetime is, all the relevant coordinate systems for Physics in GR always comes from observers and reference frames?
If not, how to make sense of coordinate systems in GR, considering all these points?