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There are a ton of verbs with multiple readings and the exact same okurigana. Sometimes they mean totally different things and sometimes they have very similar meanings, so in the cases when they have similar meanings, how does one determine the reading?
To give just one example,
堪える: たえる, こたえる, こらえる, are all listed as common readings and mean 'to bear, endure'
I agree that this is very difficult. One way I've found that usually works is to use context to determine the correct reading. Often one of the readings will have specific nuances that the others don't, so the context of the sentence can help you out.
One example that I personally encounter all the time is 汚れる. It can be read as both よごれる and けがれる. They both mean "become/get dirty". However, the latter carries the additional nuance of a moral/ethical "dirtiness"/impurity/uncleanliness/corruption/defiling. So in my Christian Bible, in places where it speaks of spiritual uncleanliness or impurity, it is almost always read as けがれる.
- 汚【けが】れた霊 → Impure/unclean/"evil" spirit
- どのような人の死体であれ、それに触れた者は七日の間汚【けが】れる。民数記19章11節 → Anyone who touches any type of dead body will be unclean for 7 days.
- 女性を汚【けが】す → Rape/Defile a woman
Doing a really quick research of 堪える, たえる and こたえる seem to mean the same, but the latter appears to be somewhat antiquated/literary. While こらえる carries the additional meaning of "supress/hold back", usually associated with some kind of emotion (あくびをこらえる → supress a yawn; 涙をこらえる → Hold back tears).
