It’s very good at modeling real world distributed systems problems and solutions, so it would not surprise me to find applications to production line design. For instance a very basic realization is that the typical throughput/latency tradeoffs have to be made.
That's effectively the question: what is the buffer size needed to insulate two unit operations without introducing penalizing ramp up and ramp down phases. If one could get such answers from Factorio that would be very funny for the 10-20k dedicated software packages.
I think that would be trivial to model in Factorio. Honestly every factory beyond beginner size is dealing with that, not always in a principled way of course.
Personally I find the new DLC with compact design on space platforms to be really fun that way. Back pressure has been a necessary mechanism to create to prevent all sorts of deadlocks for instance.
