Factorio has an extremely advanced modding API, so the codex harness has access to the game data via the client side modding LUA api to read things, it also uses the same api that is exposed as MCP tool to send Input Actions - input actions are internal Factorio representation of mouse and keyboard. It also does use screenshots sometimes to understand what's goiung on, so it's not just the modding api proxy.

Inputs wise it plays exactly as a human does, there is no difference.