The Framework Desktop motherboard does actually have a PCIe x4 slot, their case just doesn't expose it for whatever reason. But you can buy the board separately and put it in your own choice of Mini-ITX case which does.
That PCI slot has low power output, not suitable for what people would plug into it. Easier to cover it than run into support problems. It won't run a GPU directly. It will run an Oculink card which will allow use of an egpu.
I saw that, it's pretty strange.
This case is cute and well built but it does have strange quirks, see also the noisy PSU [1]
[1] https://community.frame.work/t/noisy-psu-fan/74751