What I'd really like is an RPi4 or RPi5 that has an ATmega328P on board that can be programmed and controlled from the software running on the ARM processor. Basically a built-in Arduino UNO.
It looks like the RP2040 on the X4 is connected via USB. The RP2040's bootloader mode that enables flashing emulates a mass storage device over USB to transfer firmware, so it would be confusing to not connect it via USB.
This means that your x86 program doesn’t directly control the GPIOs, it must communicate with the RP2040 over USB serial. The RP2040 must be flashed with a firmware that knows how to handle these serial commands.
It works, but it’s an extra step and timing may be an issue.
On the other hand, a Raspberry Pi Linux program can toggle GPIO pins natively simply by using the official libraries.
I mentioned the RP1 in another comment.