Hi, and welcome! You've got a good start here.
1: Unfortunately object parenting of any kind is not yet available in Terragen. You'll have to either sync manually, or generate your synced animation in another app and import with FBX or Chan.
2: I believe you should have basic alpha output. On the Sequence/Output tab of the Renderer node, make sure Extra Output Images is checked (enabled). Then use Render All To Disk and you should get a separate alpha image along with your render. When rendering test images, you can explore the automatic output files (if enabled) from the File menu and alphas should be saved automatically there too.
3: The issues you're encountering may all (or mostly) stem from use of the Coverage Adjust in the cloud layers themselves. That setting is a sort of post process on the gamma of the cloud density, so it can for example turn black into gray, meaning areas of no cloud can become areas of thin cloud when you use it, or areas that were previously masked out can now have cloud. So it doesn't necessarily preserve the incoming Density Shader characteristics that well in all cases.
What you may get better results from is using the Coverage Adjust *in the density shader* (fractal noise) itself. This will bias the coverage in the noise function which should have results much more like what you want. Try that and see if it fixes several or even all of your issues. You could also try the Final Density Modulator as a mask input (on the cloud layer) instead of masking the Density function (fractal noise shader), i.e. input your Simple Shape Shader into the Final Density Modulator input.
- Oshyan