"These suffice to let the speaker know how exactly to say the word unlike in English where it has to be learned case by case based on whatever is popular or acceptable pronunciation."

This is more due to how widespread English is, and how vowels/pronunciation have shifted over time. For example, The Great Vowel Shift. [0]

Korean has exactly the same issues, albeit to a smaller degree. There are plenty of words that aren't pronounced like how they're spelled, due to grammatical rules. 종로 as an example. Or cases where words sound exactly the same and you just need to know the context/spelling- 쫗다, 쫒다, 쫃다, 쫏다, 쫓다.

Then there's regional slang/pronunciation/dialect. Busan dialect is fairly different from 표준어, or the "official" standard language. This phenomenon is not unique to English in any way. Any language scaled up will develop these issues over time.

At least you can try to pronounce "cough" or "종로", instead of not being able to pronounce "願" at all because you don't already know the pronunciation.

[0]: https://en.wikipedia.org/wiki/Great_Vowel_Shift