After thought: Do you mean that players will have to wait until they get to the finished product before they can get a modified item and intermediate items will have no affect on that?
Yes, only the final process, the one before creating the final item will have the possibility to get a modifier.
The stacking system do not allow to stack items with a different properties, and this is good, otherwise it would be impossible to retrieve a given item within a stack.
Initial idea was to allow the gain of a random modifiers along every step of the process, however it's true the number of intermidiate items can get easily out of hand, and what would have been conceived as a feature becomes an hassle and that's not good.
How often the bonus is given also depends on how difficult is the crafting in term of necessary number of steps required to craft the final objects. There are some simpler crafting, like herbal where it's really easy to produce a final item and it doesn't take long at all. Likewise for cooking there are short recipes and longer recipes.
On top of this I should add getting to the final items instead of repetedly crafting a single intermidiate items usually gives more practice points. Encouraging the creation of final products may ideally speed up training as well. One problem often reported was the lack of primary items to continue crafting after a final item has been produced. This is why we are introducing "recyling" recipes, this will somehow extend the availability of material adding lootable 50q items to the list of items usable to train on.
In the end how often a given modifier is attributed can be controlled by setting a different chance depending on the crafting or the minimum chance to get it.