I think the machines would become a lot more flexible of inventories were independent of any input and output ports. The machine definition would need to list these inventories, and then which inventories each input and output inserts into/extracts from. Recipes could then also point to inventories, rather than inputs and outputs.

This system, for example could create a machine with a single internal fluid tank, and two item slots; put a bucket of fluid into the input and the fluid tank gains a bucket of fluid and spits out an empty bucket. Likewise, you could insert an empty bucket and the internal tank could lose a bucket of fluid and the machine could spit out a full bucket. This is just one example of many possibilities.

Added to master suggestion ticket. Archiving this ticket thread.