All the info you need is right there in the final puzzle.
The question to ask is... Jung ner lbh gb qb jvgu gur yrsgbiref sebz cntr 12 orsber lbh fbyir?
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Alright, I think I got it, but not sure if I happened to notice it by coincidence or if that is the intended way. Is the intent to see that you have duplicate letters left at the end, and then figure it out that way? I did not do this; I saw the word "won", and traced it backwards since I knew the "N" was the final letter and of course knew the total number of letters I was looking for.
Also, what is the box next to 12th word list on the final page meant for?
Yep the intent is to use the leftovers as a guide for the 12th word, but your way works fine too.
The box is just a little checkbox to mark off to affirm you've gotten the final message, in case you didn't get 144/144 in doing so, or got all 144 but missed the message due to not writing out the list.
Hmmm. The most similar game I can think of is LOCK for PS Dreams. (Although I haven't played it myself, I just watched Keith Ballard's play-through.)
I don't play a lot of word games or puzzle hunts, so everything else that comes to mind is just normal puzzle games with good epiphanies -- Linelith, Öoo, Slicecraft, Pâquerette, Bee Magic, N-Step Steve, Insight, A Monster's Expedition, etc.
In terms of books, ABDEC might be the most similar to 12 WS (consistent rules, fleshed out over time) but it is fiendishly difficult at one point. Oh, and the excel-based puzzle Rainbow Challenge / INTAO 🟥🟧🟨🟩🟦🟪⬛ seemed excellent, though I got stuck halfway through, and it's structured such that the rules change for every puzzle.