Welcome to the RetroPie forum :)
Sounds like an ambitious project.
For the peripherals: You will most likely need to use a analog to digital converter as the Raspberry Pi does not have one built-in. An external MCP3008 can handle up to eight analog inputs (and you can use up to two MCP3008 on an Raspberry Pi). This repo [1] contains an example on how to use an MCP3008, additionally you should enable SPI on the Raspberry Pi [2].
The sources (pedals, aso,) should be able to be run with 3.3V, as this is the allowed logic level for the GPIO. If they have to be do run at higher voltages you will need a level-shifter [3], for example BSS138 MOSFETs are suitable for this. If you apply more than 3.3V to the GPIO logic gates it may damage the Pi.
[1] https://github.com/chunksin/analogjoy
[2] https://raspberrypi.stackexchange.com/a/48234
[3] https://www.digikey.com/en/blog/logic-level-shifting-basics
For the SBC: If you have a Libre Potato already you can start with it for the prototyping with the peripherals (see above). Howerver, the GPIO pinout is not compatible to the Raspberry Pi 3 or 4. Thus it will include remapping when you switch to an Raspberry Pi.
As this is your first project I would refrain from using a different board than a Raspberry Pi, to reduce complexity. Although a Pi has a higher price than a Libre it will save you worries, head-banging and tinkering time in the long run. I do not own a Libre but I read the GPU is proprietary (Mali 450), also Libre Computing does not provide a Debian Buster (RaspiOS 10) image (only Bullseye, RaspiOS 11). [4]
Currently RetroPie uses Buster as OS, Bullseye support is in the works. This means: You will have to adapt the RetroPie-Scripts and esp. GPU related configuration by yourself when you run a Bullseye RaspiOS + RetroPie scripts on the Libre. Plus the usage of a libre computer is at best a niche in this forum, i.e. expect little to no support. If you can afford it head for a Raspberry Pi 4 (2GB is sufficient) as it has enough performance to run racing simulations with theses systems: Sega Saturn, Sega Dreamcast, Playstation 1 and earlier consoles/home computers. However, emulating Nintendo Wii and Playstation 2 games is not possible (Running Nintendo DS games smoothly is a hit-and-miss).
[4] https://libre.computer/downloads/aml-s905x-cc/