Currently the stockpiles and workshops have two settings "Take from anywhere" and "Take from links only". OK, stockpiles have those settings and workshops will either take from anywhere or only from linked stockpiles if there are any, but apart form the option being hidden, it works the same.
One problem with it is that for custom items and reactions, you need stockpiles for schematics and other auxiliary items, such as barrels / pots and not just for the most obvious reagents. This could be improved by having a setting for workshops and stockpiles "take from links first". Like the name says, it would first check the linked stockpiles and only take from anywhere else if it can't find what it needs. One downside I see is that with something set on repeat and an empty stockpile, random items would be used for that reaction, which is basically the same as before having links. Anyway, you could have a linked stockpile with exactly the type of item you want to process and not have to worry about containers, tools, schematics and the like.
Or maybe have a mason shop with a small stone stockpile with wheelbarrows, so that the mason will only take long walks to collect stones when the stockpile is exhausted and no jobs will be cancelled.