Adafruit FT232H Breakout - General Purpose USB to GPIO, SPI, I2C - USB C & Stemma QT: https://www.adafruit.com/product/2264
Adafruit MCP2221A Breakout - General Purpose USB to GPIO ADC I2C - Stemma QT / Qwiic: https://www.adafruit.com/product/4471
The downside is that code becomes slightly more complicated, the upside is that it makes easier to replace the Mini PC with a totally different one, or even emulate it in a VM then connecting the GPIO board using USB pass through.
Rethinking GPIO can also open more possibilities such as putting them beyond a network (say Arduino+ENC28j60 and similar ones for Ethernet, ESP32 for wireless, etc); of course having them outside the main CPU will imply some speed and latency issues, although I'm sure they would remain unnoticed for many non critical use cases.
My question would rather be why the RPi when there are better SBCs out there, but that is my personal taste and the Armbian and DietPi communities being more than enough for me.