Those models were created with hundreds/thousands of bones. It's very complicated to set up and there is nothing in the Source Tools to help you there.

Vertex animation is actually supported if you target a recent enough engine (Portal 2 probably doesn't qualify), but it's an engine hack intended for Source Filmmaker and probably wouldn't behave correctly in a game.

Give me tabs or give me death!

This was fixed in version 3.0.2.. If you really are sure that you are using the latest version, please upload your .blend file and I will take a look.

That's an error from the model compiler. It's almost certainly wrong to suggest that write permissions are the error, instead it will be trying to read the file without first checking if the folder exists.

I'm pretty sure nothing has changed regarding this...

That looks a lot like an internal Blender error. Perhaps try a clean reinstall with your profile deleted?

I'm a little reluctant to change something so fundamental that has been in place for so long, but I could provide an option somewhere I suppose.

If you feel comfortable editing script files, you could open export_smd.py and change line 532 to read:
This will cause animation exports to have the same bones as mesh exports.

There is probably an invalid character in a bone name slide your SMD file. Try editing the file in a text editor and changing any bones with unusual names. It will probably be obvious where the problem is.

It's intentionally worked this way since the 30th of January 2014, but I can't entirely remember why.

It might be because an animation can be applied to multiple meshes with different deformation settings, so we can't safely decide what to cull. Or it could be related to supporting the import/export of animations without any meshes in the scene.

This shouldn't break anything though. The compiler can handle collapsing bones perfectly well. What is the exact error message you are seeing?

The tools currently know about these three vertex map names:

VertexPaintBlendParams$0
VertexPaintBlendParams1$0
VertexPaintTintColor$0

If there are more, please point me toward them.

This will be fixed in the next release.