Always keep in mind that one of the harshest limits on PC design is the number of pins on the CPU.
I really doubt we will see GPIO pins available directly from the CPU, and if they don't come directly from there, there isn't much difference from using a PCIe or USB adapter.
Or, in other words, what you want can already be done about as well as it will ever get. The hype for adding FPGAs into PCs is for using them as co-processors, completely inaccessible for any other hardware.
AM4 has 12 dedicated GPIO pins and ~30 pins where GPIO is shared with other functions. On the other hand these are mostly meant for platform control, and maybe blinking LEDs, not for user-space bitbanging something there.
Also of note is that both Ryzen IODs and Intel PCHs contain what could be called "half of an ESP32" connected to few IO pins under the name of on-board HD audio.
I really doubt we will see GPIO pins available directly from the CPU, and if they don't come directly from there, there isn't much difference from using a PCIe or USB adapter.
Or, in other words, what you want can already be done about as well as it will ever get. The hype for adding FPGAs into PCs is for using them as co-processors, completely inaccessible for any other hardware.