I do not fully parse your answer, or rather don't see the actual answer in it. Why, do you suggest, do I not see the clouds gradually fade in and what will I have to do, in order to have them so?
As I saw yesterday, my answer is obsolete - the shader now gets the cloud visibility distance as parameter in recent GIT, so clouds fade smoothly whenever they reach the edge of the visibility limit.
Again, I don't understand you. Why do you say that passing transparency to the shader of convective clouds is unbearable while you alegedly do so for all the other clouds (as you, so I think to have deciphered, implied in the first paragraph of your answer)?
Do you have a rough idea how the two weather systems in Flightgear work? I assumed you have that knowledge, but if not then you may want to read this up in the documentation (README.local_weather.html, README.3DClouds) first.
The shader doesn't get a transparency value passed, it knows the vertex position of the cloud relative to the eye position, from that it computes a distance, and from that distance it computes an alpha value. For a cloud suddenly forming at a closer distance (which you'd like to fade in over time), a distance criterion does not work - this needs the time dependence of the alpha channel explicitly passed to the shader from an external source.