This kind of bitpicking is the essence of premature optimization. All that to "indirectly" improve FPS? As always: don't trust your intuition, trust the profiler.
1) I didn't say anything about bitpicking. I said making stacks of like objects, and also making more objects alike by getting rid of 573 types of leather and so on (or wood types) when most people don't care (or implement a system for indicating special "artifacts" where you do personally care for nostalgia, and those alone). That could be a 100-fold reduction of items in game, easily. That's pretty macro level stuff. Nary a bitwise operation was mentioned or implied.
2) Premature optimization is optimizing before you know the bottlenecks and/or before you even have working code. Toady has working code already. And people have complained and profiled sources of specific bottlenecks already. Item count is one of them. Masterwork has in fact already even gone in and reduced the redundant types of leather and has already demonstrated that this speeds up code. It's not even a theoretical fix... (my suggestions do go beyond that, and are partially theoretical, but I don't have the code to profile it myself, it is assumed Toady would do that yes).
3) I don't think you can apply normal concepts of "premature optimization" to dwarf fortress, anyway, even if it might normally be considered slightly premature before a whole program is finished. Because there are already thousands of people playing it every day. Unlike a normal program that exists only on the programmer's computer when halfway done (and maybe a few special testers), this is already in the public, and there is a reasonable expectation of doing macro / major types of optimization now. Not at the end. Because by the time it's finished, it's entirely possible that 70% or something of all the games ever played will already have been played! It would be dumb/kinda obnoxious to optimize only at the end and abandon the people playing it for the 25 years beforehand... Also impacts donations, of course.