I can see why the game came with the underwhelmingly small cumulus clouds. Being represented as an agglomeration of textures, visually they behave differently from a modeled object, like a plane or building. The best way to see this? With this Big Cloud mod installed, go to a wide FOV of at least 90 degrees. Observe the overlap region between any two fairly close clouds when you are very close to one of them. You will often find the cloud edge changing position VERY significantly! Often times going from full overlap to wide clear sky gaps. So just by swinging your gaze (especially with head tracking) you can alter the obstruction and see past the clouds where you should not.
The underlying reason is this. Simulators use the gnomonic projection, the characteristics being well seen at very wide FOVs beyond about 90 degrees. The enlargement for far off-axis angles becomes considerable. A 'sprite' is not similarly stretched, and so with increasing off-axis angle becomes progressively undersized with respect to the landscape and other objects built upon polygons.
The cloud modelling seems to strive to overcome this by building a cloud from a number of textures in their own little cluster. But when you get close to such a cloud, the angular separation between some of these texture centers can become large enough for the differential stretching to have an impact.
The cure--outside of modelling from polygons--is a more densely populated cluster of textures as view distance decreases. But of course the issues of frame rate lowering must be considered.
And so right now one should not employ very large FOVs when close to these clouds. My 'default' is 105 degrees, which well reveals this odd behavior. But I don't like a smaller FOV, except when zooming for detail for limited periods.