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I mean. yeah. That's "just" a very technobabbly way of saying they're taking matter and turning it into energy and back into a different sort of matter.
Basically, mc^2^ --> e --> = mc^2^.
For consideration, a 6 oz steak would have something like 15.3 million gigajoules of energy getting spat out inside of a few seconds. I'm not sure how that stacks up to the ridiculous numbers of the warp core, but in more realistic numbers, it's probably the single largest source of power on the ship.
Now, it would seem you're correct that they're not using some sort of procedural generation and using analog voxel maps. It is important to recognize that the TMs are secondary sources that may or may not even be canon. I'm willing to just say that ST's engineers are amazingly, brilliantly stupid, though. (See: seatbelts. See: surge protection.)
There is no technical reason they couldn't procedural generate their materials using some sort of materials libraries describing the materials and how they're to be generated. LAAMPS and GROMACS were out in '95 and '91 and do exactly that. LAAMPS is a more general system for modeling atoms (and sub-atomic stuffs,) and GROMACS is specifically about protein modeling.
You could even, presumably, generate new and interesting molecules just by coding to generate new and interesting atomic properties. (like maybe Neutronium? that'd be exciting.)
For comparison, think of a Sierpiński triangle. you can generate the fractal pattern using c with just a few lines of code. The jpeg image of that would be a much, much larger file. Especially, for example, if you went down to atomic scales across say, a 18"x12"x12" build volume. There's a reason modern gaming is now using procedural generation for all of their worlds now. Especially in games where every new map is different. (mine craft, for example.)
and then remember that every variation you could think of would suddenly get prohibitive. each one of those 37 varieties of tomato soup would have such a size. imagine the ice cream library. imagine literally everything. And then imagine every time they have to figure something. Like. Uhm. Worf's second spine. (it's all just chemistry.) or like in DS9's Tosk episode when O'Brien had to replicate the Arva Node (?) for Tosk's ship. That's not something you can just scan down and spit out a new functional thing- it's broken afterall. And if Tosk had a spare, he'd not need the station's services.
Or like, to accommodate "Steak with extra asparagus" or "double butter on the mashed potatoes". all of that could just be a variable in the program script producing the pattern.