Since the material applied to the cube where the clouds are drawn is sort of translucent material, it suffers from sort issues like any other translucent material. Inside the BP_CloudscapeViewer you have a component mesh called CloudscapeMesh, click on it and at the details panel on the right search for “Translucency Sort Priority” which has a value of 999 (default is 0). This value tells that the cube mesh must have priority on the sorting among any other translucent material elsewhere.
So to solve an issue like yours, you need to change the “Translucency Sort Priority” to a value higher than 999 for any other mesh which needs to cover the clouds. For a particle system, you can only change this value at its instances dropped into the level!
Cheers!