There are two issues.
1) Apple Silicon won't support PCIe.
2) Apple doesn't want it to.
#2 means Apple is taking nVidia and AMD head on in the GPU space. Apple wants to control everything, and allowing these competitors on their platform is giving away too much. Because Apple Silicon scales better than competitors' hw, the desire for third party GPU is probably going to evaporate within a few generations of Apple Silicon. I mean, we'll see, but that is my best guess, because it seems like that was an intentional decision rather than oversight.