When you can see part of the map through a skybox brush, it's because the visleafs on the other side are visible. To block visibility between areas, your best bet is to put an areaportal in each doorway between your different jumps and make use of hint brushes to block visibility as best you can.
If that doesn't get you what you want, you can make the hallways between areas longer/add corners, as well as just put teleports between each jump so visibility isn't even a question. A lot of jump/surf maps use both of these techniques, both to block visibility but also to make falling into a previous stage more difficult.
Basically, don't try to treat the skybox as a physical wall that things can hide behind. It's air. Air that just happens to be solid, and can mess with the visibility sometimes but mostly when you don't want it to.
Basically, don't try to treat the skybox as a physical wall that things can hide behind. It's air. Air that just happens to be solid, and can mess with the visibility sometimes but mostly when you don't want it to.
While that logic makes sense for most maps, jump maps in particular have really large open spaces that don't tend to make much physical sense, plus players will be way high up in the air. For some maps this, this logic would require rendering everything at once or putting giant walls up.
(EDIT: As a side note, this is part of why designing connectors to block sightlines is desirable. If you can't ever see from one major outdoor area into another, then you'll never have rendering issues like this. Some maps will use this to their advantage and create buildings that only appear on one side of the sky.)
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