“If I ran the business” (TM), I would just put it in Factorio settings as a toggle switch called “Reduced Security Mode - Allow Lua Bytecode.” By default, it’s turned off. People who really want those mods can turn it on, as long as they are informed (UAC prompt style) that they better trust the mod authors. I’d also add an API for mod authors to detect if bytecode access is enabled; so they can make their mods compatible with either environment.

Or maybe, down the road, Factorio could enable mods with greater privileges, as long as they are open source, and do an App Store-style review process with the community. Approved mods get not just bytecode, but perhaps even some of the typically forbidden modules like filesystem access. Unapproved mods using those enhanced privileges won’t run without a startup flag.