I would again recommend
people watch the Extra Credits episode on Choice and Conflict when they want to talk about meaningful choice versus simple calculations.
You say that as if it's trivial. If you are extremely luck and get a blacksmith mood, maybe. Otherwise it's by training and then you know what to do for a decade (ore, fuel, hauling, remelting,...) . Plus, that blacksmith needs good tools to make masterwork tools himself.
I do say it as if it is trivial because it is still trivial.
Every player will train their legendary blacksmith
because there is no reason not to, and it provides a game benefit. Upgrading your facilities when you get a benefit for doing so, and its costs are trivial means there is
no reason not to do so, and in that case,
there is no true player choice, it is just a calculation.
Much like how making crops take longer to grow does not actually make "farming harder", it just makes you have to designate bigger fields, making tools and upgrades take longer does not make them harder to achieve, nor any less desirable. There is no more effort spent training up a mason or carpenter or blacksmith with your system than there is without your system, and players would want to do that anyway - why would they suddenly start wondering if maybe it would be a good idea to shoot themselves in the foot by
not maximizing production now?
Players will set their dwarves to creating random junk to max out the dwarf skill the way they've always done because you've done nothing to disincentivize it. Sure, they'll need to jump through more hoops to get the upgraded levels of tools, but that is not really any choice. That's just adding in occasional needs to punch the "upgrade tools" order at the appropriate time for maximum efficiency, which is, again, a calculation, not a choice.
Again, there is absolutely no reason you would specialize, which makes the specialization argument moot - if you can create masterwork metal tools for one job, why not create masterwork metal tools for every job? Why would you choose to hold yourself back on one industry just so you could say you were "specialized" in another?
Sure, you could just make less of that type of industry's workshops in general, but that is something that we already do without tools, which, again, makes the entire argument of specialization or choice invalid.
Honestly, however, I view the entire "choice" argument to be a secondary or tertiary one that exists solely to back up the real primary goals of those who are arguing this thread in the first place, which is the aesthetic/realism argument above.
The rationale of this being a "choice" is obviously flimsy, as it is even less of a choice than what beehives give us - beehives give us choice of how we plan out our honey-production centers, with the added actual complication that they must have access to the unprotected outside, which makes them a much more challenging thing to plan for than the simple order in which you create your sets of tools. Virtually
anything with a spacial element to it has more choice than a "spreadsheet problem" of supplying your dwarves with an adequate number of items in each data cell.
Again, I believe this shows the aesthetic argument above is the real motivator, since if you were really trying to introduce player choice over micromanagement, then you wouldn't be spending your time talking about how interesting you found a choice between making a chisel or a pair of tongs. No player is going to be seriously distressed over that choice, they're just going to order both made if they need them both.
The choices that serve to further the core gameplay of DF are choices like how you excavate or build your fortresses. Having farms you have to excavate, irrigate, and manage add real choice in how you set about doing that task, as does whether or not you replace or supplement farming with animal ranching, and what animals you use to do that. Even honeybees, and their need to access outside tiles are a meaningful choice. But what order I build my chisels and tongs in, much like the order I build my clothing in, makes very little difference.
In fact, I can replace my reaction in the loom to create individual clothes with a simpler reaction that takes 3 cloth, and produces shirt, pants, and shoes (the only clothing you need) all in one reaction, and it would have no real impact on the way I play the game. That's because the order in which I build my clothing is not a real decision in the game. Nor is the choice between building table or chair first. The choice of how many doors I build in a ratio to tables and chairs is only a blip on the radar. How many logs go to beds rather than bins or barrels is a minor balancing act important only for not running out of any of them, and a tedious micromanagement task that should be taken off my hands by Standing Orders. These, and tool construction order, are not real choices, and are the sort of thing we should avoid adding onto for the sake of our sanities. They only serve to add to the tedium that one must suffer to get to the good parts of DF. Nobody loves the need to manually designate individual wall pieces and their materials over and over again, so those are the portions of repetitive, tedious, micromanagement "gameplay" (more like work) that should be avoided at all costs.