I don’t know, I like the idea of the workers doing the heavy lifting and the crafter doing the crafting, which I think was the original concept behind the crafter output stockpile. The only problems with the system are having the goods not moved from the output pile to the general stockpile (a bug which will be fixed) and the inability to move or remove the output stockpile (an obvious feature to add if they stick to the current system). So, I think it would be fine to just fix these issues and stick with what we got.
However, perhaps a compromise would be possible where the crafter is not reliant on having their own output stockpile—if there is none, they just move it to the nearest acceptable general stockpile. Given that, I like the third option suggested by @easto1a. You can remove and create crafter output stockpiles freely. Every player will be able to stick to their own preference that way.