I think that the apoapsis above 0 is because it's measured from a specific level of reference, unlike the height that takes the reliefs into account. For example, look at the apoapsis of my Curiosity rover after it climbed the Olympus mount on Mars:
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Just for information, the Olympus mount is a mountain that actually exists on Mars. It's 25 km high, and it's the highest one in the whole solar system.