I think this might have popped up in a previous bug thread about improper rate calculations vs actual rates.
The effective productivity of a machine increases when the machine exceeds the 60 tick limit for crafting recipes, i.e. crafting speed > recipe time * 60.
For example, I'm playing with Krastorio 2 crafting recipe is 0.5s 1x copper plate -> 2x copper wire. My assembling machine has crafting speed 58.25 and productivity +40%. This mod calculates the theoretical rates, 116.5 input 326.2 output. However, this exceeds the tick limit of 60 recipe crafts per second. The actual input of copper plate is 60/s since each craft uses 1 plate x tick limit. But, the actual output rate is not 60 * 2 wire * 1.4 productivity per second.
I did some tests using numbers from the production stats panel and came up with a formula.
actual productivity = crafting speed / recipe time / 60 * productivity
- 60 is from the tick limit.
So for my example, actual productivity = 58.25 / 0.5 / 60 * 0.4 = ~0.7767
Then the actual output = 60 * recipe output amount * (1 + actual productivity) = 60 * 2 * (1 + 0.7767) = 213.2/s copper wire
Note that I did not test this formula extensively. I tested, using creative mod to avoid input and output limits, on two recipes copper wire and sulfuric acid.