I love this idea with thrusting passion.
I think basic/starting workshop designation could-and perhaps should-be kept as simple as it is now. You tell your dwarfs to build a kitchen or a mechanic's shop, and they do just that. Once they've "created" the basic space, you'd be able to stock it with tools, larger pieces of equipment, shelves, chairs, workbenches, whatever you'd like.
It wouldn't have to be a matter of looking up in the DF guide what tools you need to build, say, a carpenter's shop. You could just build one, and then progressively make it more and more sophisticated, over time. That'd also give you the advantage of "fine-tuning" the basic shops into ones that fulfill different purposes: One carpenter's shop might be all about fine musical instruments, while another might be a boat-builder's workshop.
Each could still perform the same basic tasks that you would most use in your Fortress, but for the least-used and most specialized tasks, you could outfit a very advanced--and very expensive--shop, once, instead of paying to equip 3 dozen shops.
To remove the need to hunt for your specialty shops, the game could employ a simple search engine, where you'd input the task you wanted performed, and then the engine would locate each shop that can perform that task, from nearest to farthest away.