Aye, the Aria manga has a lot of them. For example, it’s set on Mars, but a Mars that has been terraformed to the extent that it’s now covered in water, so it’s been renamed Aqua. When’s used in dialogue, though, it’s usually written as 火星 - it’s telling the reader that what they’re saying is “Aqua”, but what they mean is Mars. Similarly, when they refer to the Earth, it’s written as 地球 - what they’re saying is “Manhome”, but what they mean is “Earth”.
But yeah, sometimes you can use one kanji’s reading to give a different kanji a different subtext. Like… um… 山田 - the speaker is referring to Yamada, who is standing next to them, with こいつ, but to make it clear to us that it’s Yamada who’s being referred to, his name is included as well.