[2023] Auto function overkilling my inventory?

Sounds like everything is set up fine. One thing to keep in mind is that some blueprints create x items. So, the well water for example, will produce 60 for 20 jobs. That still doesn't explain you having 1k+. The version of the game that's in the works overhauls a lot of that automation stuff and it should be much more accurate. That said, I'll do some extra testing to see if I can find any oddities in that auto-job.