To illustrate how the meaning of 玉 varies with its yomi, let’s look at one graphically simple but linguistically complex word:
玉石 jewels + stones
When read as tama-ishi (using the kun-yomi of both kanji), 玉石 means “boulder.” But when read with the on-on combination gyokuseki, 玉石 means “wheat and chaff.” Instead of separating the wheat from the chaff in Asia, they separate the gems from the rubble. Makes sense. If you worked hard to separate the good from the bad, what would you rather have at the end of that process—rubies or wheat?