In my own game I use a box, this box looks not like a person but an object, since npcs tend to change direction a round or circular object model could be used to represent the crafting table or tool for instance. This way it would present the player with the feeling they crafted this object and not the NPC.

Currently void items are created from the materials you gather by a NPC.

There is a sense of achievement when you remove the NPC person and place a NPC like object that represents a tool.

The way to add craft skills is similar to learned skills like lockpick and that you would gain experience crafting armors, weapons, potions as each time like reading a scroll you gain a proficiency level increased. Higher levels cloud allow more results or so scroll crafting or scribing would create from the materials instead of 1 scroll, 2 scrolls and then 3 scrolls. Giving players a new way to gain and achieve results.

To include the professions menu a tool could be added like a mortar for potions which increases the possibility of instead of 1 pot per material used to 2 or 3 based on the level of profession skill.

I'm all for improving Xenimus however, I fail to see how comparing it to or taking aspects from a 20 yr old open source failed project is going to improve anything. Not to mention E.J. is already working on the crafting and we have yet to see the full fruits of his labor. As for changing the NPC to a crafting station, I personally see no difference.