Hardly a feature. Just poor programming. I highly doubt clouds are meant to pass through solid walls and buildings. If so, whoever came up with this as a "wise" idea was a fool. Obviously shortsided on someone's part in never expecting skyscrapers or sky cities to be built. I am at odds to why modders can fix these issues in a matter of days, yet the core team can't fix something like this in years (back when Notch decided that this was a good idea and should be fixed).
I hear the argument that it would add to CPU "strain" but obviously stars, sun, and moon circle around the world but don't travel through skyscrapers and high structures. The question is why clouds couldn't be inserted into the minecraft stratosphere where stars reside.