These are some very obscure errors. Please upload your blend file and I'll take a look.

You can attach all three meshes to the same armature with the Armature modifier. It doesn't matter much which objects are parented to which.

Can you upload the QC and models somewhere, please.

Don't hold your breath. I can add name remapping on export to work around this, since long shape key names are a hard requirement.

Oh right, that stuff. It was never supported for game animations before, only SFM, but it looks like that has changed now. Can you upload the DMX files for your model and animation above?

If I understand you correctly, this is already supported by the Vertex Animations feature. You can add one from the Source Engine Exportables panel.

It's not just working with other programs that causes trouble, it's interacting with the data that they produce. If the importer messes with the bones in the reference mesh and then you try to import an animation later on, the imported data will be junk.

If you want to just make a tweak to a model and then use it with the same animations as before, a very common use case, then the bones need to round-trip correctly.

Creating Blender bones isn't just a matter of rotating things, either. Bones do not actually have a rotation, but a head and a tail location. And that head points up to the parent bone. It's frequently impossible to generate a good result programatically because the script doesn't know where to put the other end of the bone.

Properly converting skeletons to Blender's wacky skeleton format is destructive and for that reason will never be done by the Source Tools. You are free to write a second script that does the work, but it won't be easy.

I can't reproduce that with a test scene with three shapes on a cube.

Do you have your own flex controller block or are you letting the tools generate one on export?

Can you upload your .blend file?

I've tried to use cloth_enable in the past but never had any luck. What effect does it have? (I don't have access to a Windows machine at home right now.)

That is quite painful. I'll look into it.