Clouds/sky/weather are legacy systems. They work how previous devs made them and then we refactor them to better meet the final design of the game. The why of designs is often lost and in the end I don't care, we just need to make it work to meet the goals of shipping the game. I've been cleaning up and rewriting those systems as time permits, but it is a big WIP.
Some of what you describe are just side effects of a combination of things and it may change by the time we go gold.
Test features are usually for debugging and generally don't become normal features. I'm not sure w