If you really, really, wanted to make it so that you could add items to a stack individually, I think you could drastically increase the number of stacks. You would need a reaction that specifically takes a reagent that represents a stack of two stones and a seperate stone that is somehow of the same material(not sure if you can save the material used in the first reagent to require it for the second) and produces an item that represents a stack of 3 stones. You would also have to create an item for each stack size. And there would likely need to be counter reactions that completely disassemble the stack, or just take one stone out.
And then you have to wonder if you want to be able to take 3 stones and make a 3-stack straight from there instead of requiring the second stage.
It seems like it would just take up a ton of space in the reactions list for a workshop, though you could create one specifically for that purpose. And I think I'd suggest making all but the first step automatic, and perhaps only disassembling 10-stacks, which could be done completely. That way, you can just tell a dwarf to start a stack, and you get the joy of seeing him start it, grab another boulder, add it, grab another boulder, add it, etc. until he's added 8 boulders to the stack. If you don't have enough, say you stack all your stones and end up with a bunch of stacks of 10, and one of 6, then the next time you break a stack down, 4 will be taken from it to add to the smallest one. I also think this method would bug out if you put 2-stack on repeat, even if it adds the other tasks to the list. The completed tasks would go something like: 2, 2, 3, 2, 3, 4, 2, 3, 4, 5... so you'd probably end up with a ton of different sizes when it finished.