If tool and equipment quality affects work speed and final product quality, then "workshops as areas" would make upgrading them less hastle, as you could just place a new anvil/table/etc in the area, rather than having to deconstruct and reconstruct the workshop building each time.
Another advantage would be is some jobs didn't use all the equipment in a workshop, then multiple dwarves could work there simultaneously.
Example: forges and smelters are combined into a single "smithy" workshop. To create a smithy:
1) Create a "smithy" zone.
2) Place an anvil in it.
3) Place a furnace in it (this could be a mason-created item).
4) Optionally, place box in it. (This is where tools, and possibly reagents would be stored).
Some metals can be beaten without heating, so you could have a smith beating out native copper blades while a furnace operator smelts ore to produce better metals. Additional furnaces and anvils could be added as your industry expands.
The bootstrapping problem could be dealt with by making the "necessary" equipment not absolutely necessary, but giving a speed and quality penalty to any jobs done without them. (E.g. 5x time and zero-quality only).
We can imagine Urist McMastersmith arriving as an imigrant to a fortress, only to find they embarked without any anvils or metalworking tools. So after rolling his eyes, he dumps a pile of charcoal on the ground, ignites is, and uses to heat up some iron bars, which he then bashes into shape using some handy stones (which, as any adverturer knows, can be found just about anywhere). After several days of this, he has a crappy, no-quality-modifier anvil and smith's hammer.
Now, he can get to work properly, although he still can't make his best items as his tools are sub-standard, so after banging out a few copper axes for the woodcutters (who had previously had to resort to pushing trees over, because they had traded their axes for booze on embark), he makes a better anvil and hammer, installs them in his smithy, and gets to work.
Meanwhile, he has also apponted an apprentice (i.e. the player has activated metalworking on another dwarf), who can use the old anvil.
If anvil quality affects product quality, e.g. by granting an effective skill boost, then the relationship between skill and product quality would need to be adjusted to keep the overall work quality balanced. There could also be a limit to how much of a bonus a dwarf can get, based on their current skill. So a dabbling smith gets no bonus from an anvil, and a small bonus an -anvil-, but higher quality anvils don't give any more benefit than a - one. A legendary smith, on the other hand, would get increasing bonuses from anvils all the way up to masterwork (and/or, maybe get a penalty for using inferior quality anvils).