As the OP, it’s encouraging to see some discussion. As I posted way back I owned a Sim that had this entirely natural and realistic cloud effect built in. It was highly immersive. The lack of it in MSFS was for me, a major disappointment when checking it out for the first time. It’s ideals were not as high as I had hoped.
In MSFS the planes and the clouds exist in two separate environments, or virtual spaces. Interaction between them is a clever illusion. Let’s give credit where due. At the moment we cannot observe aircraft entering or emerging from cloud as we do in the real world. More importantly as potential inflight threats
I may be a Military-trained pilot but I’m no programmer and suspect that to solve this problem would need a re-designed DNA (core) for the entire sim. But or course, I hope I’m wrong.
‘Sadly’ most users will probably be content to carry on as is.
But we can dream, right?