That all sounds plausible, but are we sure we're not giving too much credit to the MoS writers?
I think to think of it as "help" more than "credit." In order for something to be plausible, or to be more precise in order for it not to be implausible, its only necessary that there exists a reasonable explanation that fits all the facts. Its not necessary that the creators presumed it or believed it or were even aware of it, only that they did not explicitly disavow or contradict it in their content.
I like to think of myself as a "constructive nitpicker." Its a personal preference of mine that on the one hand I like to think about things in a way you might call nit-picking. But I like to take those nitpicks and see if there's a way to turn them on their head and make them strengthen rather than weaken the original content. The Peter David novel
Vendetta is something I consider a commercial example of this kind of thinking. It starts by looking at the Trek TOS episode The Doomsday Machine and asks a pretty simple question: if the Doomsday Machine moves around so slowly, how could it come from another galaxy as Spock suggests in that episode? And the answer is: it really shouldn't have: it would take too long and there's no way for it to fuel itself during the trip between the galaxies. That seems to be a nit pick plot hole. But what if that nitpick is flipped upside down: what would explain those facts? What if it came from outside the galaxy not because it came from another galaxy but because it had been put there from originally inside our galaxy? Let's keep going: maybe it was put there because its creators were essentially throwing it away. Why? Maybe because it was a prototype: clearly it wasn't a very good Doomsday Machine in actuality: although it did destroy many planets and wrecked havoc with two starships, really as a true Doomsday weapon it wasn't difficult to destroy. A really big fusion bomb thrown down its maw did it: during a full-scale interstellar war that wouldn't be considered a big price to pay to take that thing down.
Okay, so we have a prototype weapon that moves around slowly and destroys whole planets, mostly ignores small warships, has an impenetrable hull, no crew, and a single powerful antiproton weapon. What sort of foe would this be useful against? How about the Borg? The Borg (at least as originally envisioned) didn't care about individuals, didn't fly around in small warships, primarily targeted technology and planetary cultures, used high technology cutting beams to slice up interesting technology, and assimilated the beings of the cultures it tried to absorb. The Doomsday Machine seems almost specifically designed to be an antiborg weapon in retrospect. Its design is actually kind of silly if its enemies were anything like the Federation: its slow enough to allow its enemies to mount a defense, and its weaponry, outside of surprise, its not really good at destroying fleets of enemy warships. But against the Borg, that usually come at you one at a time in large colony ships? And assimilate whole planets?
Once you take the nitpicks apart about how the Doomsday Machine worked, how it functioned, how it moved, how it attacked, what its weaknesses were, and instead of saying its nonsensical ask instead what circumstance would make those actually make sense, an interesting idea emerges. That's what I consider constructive nitpicking. We *know* the writers of the Doomsday Machine were not thinking about the Borg for obvious reasons. But that doesn't mean there's no value to thinking it for them.