Since MM processes a recipe based on input, with some similar recipes you could end up crafting the wrong item if an ingredient runs out of stock.

Could the controller give an option to Lock the current recipe, or Select the recipe to be made?

example:
The Doodad Machine
Crafts Iron Doodads out of Iron Ingots, and Advanced Doodads out of Iron and Gold Ingots.
If the Gold runs out, the machine will use the Iron to make Iron Doodads as that's the only recipe that then matches.
If the MM can be locked to only crafting Advanced Doodads, it will then not process the excess Iron into Iron Doodads.

Added to master suggestion ticket. Archiving this ticket thread.