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Notes -
The pitch accent has far from enough information to actually disambiguate heavily-overloaded phoneme sequences, especially with projected-down Chinese vocabulary. One of the more well-known pairs is 科学 (subject-learning = science) and 化学 (change-learning = chemistry), both read identically as kagaku with a down-pitch after the ka. In an informal context (like students chatting about what they are doing), people often resort to deliberately misreading the latter as bakegaku, essentially just pronouncing the "change" bit using a slightly amusing native reading (bake- is "change" with a heavy connotation of "shapeshift", like masters of disguise), perhaps similar to saying "Lifeology" for "Biology". (Imagine a scenario in which this word was overloaded in English, with "Bi-ology" denoting the study of things that come in twos)
Once you get to heavily overloaded sound sequences like koukai, my dictionary gives over a dozen of words that are read as that with no down-step (like 公開, "publicise", or 更改, "revise"), and at least two that have that reading with a downstep after the ko (後悔, "regret", and 航海, travelling the sea by ship). All of these are common words and you could easily construct contexts where there is ambiguity between them.
For native words, the collisions are fewer, as you have to distinguish between genuine collisions (kami (downstep after mi) as in paper vs. as in hair) and ones where the two words are actually the same etymologically but educated writing demands using different Chinese characters, such as kara[2] = 空 (empty) / 虚 (hollow) / 殻 (husk) or kiku[0] = 聞く (hear) or 聴く (listen) or 訊く (ask). The latter is a fascinating topic in itself, connected to the same thing I hinted at above with writing in these languages also being an act of translation! (Compare to how any EN->RU translator has to decide whether any instance of blue is синий or голубой, or maybe an SE->EN translator has to think about whether a "stark sås" is spicy or just strong.)
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