Players generally don't like the idea that if they set up a component production line, it will consume inputs until every machine input and output along the way has a full stack of intermediate products. As a result, they tend towards overly-smart logistics networks like AE, where the network is in charge of putting exactly the right inputs in so that nothing gets wasted, but I think that it would be nice to have the Factorio-like option of letting full inputs produce natural backpressure with an acceptably-low overhead, so everything can pull directly from storage.
So, I suggest a "stack size limiter" upgrade. If N > 0 are present in a machine, then it will only accept N * one craft items in each input, and will not process if any output has more than (N - 1) * one craft items. Having modes to only affect input or output would also make sense.
I don't know how best to handle cases where different recipes take different counts of the same input item, perhaps a "recipe lock" upgrade would also be useful.