<1. While it does eat planets, it takes a long time and breaks it off piece by piece.
2. It has mechanics in place to convert planetary materials into fuel and other substances. Emphasis on other substances.
3. It has lasers and everyone knows the best mining is done with lasers.
So why does it have a city on top? Well you need homes for the crew. Clearly this was all built before Calus was exiled as all the architecture isn't rugged on the outside.>
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The Leviathan is a Prison ship meant to serve literal vehicle of Calus' exile. Over time it's implied Calus pretty much had the whole thing rebuilt.