Cool cool cool! Very curious to see this develop!
Re: the schematics. If you want to pursue this , I'd say make it into a very basic subsystem, nothing too fancy. Provide players with some very basic shapes and symbols that communicate different interpretations of a schematic that can be combined or altered. Agents add their own layer of symbols/shapes through some kind of oracle system or table generation? Like you said, it's not about simulating real schematics, but emulating change over time. Given that this is a 3 week jam though, there is a danger of it succumbing to feature creep.
Not sure if this helps, but I did come across this thing: Sigil Generator by watabou (itch.io)