Just select only reference mesh in object mode and expot it.

Rotate it?

Sometimes It's better to import just reference model instead of whole qc so it won't be messed up on scene. Some qc's might be very complicated to handle them properly.

The problem is that BST exports smd's with bone weighting. GoldSrc doesn't support this. That's why your "bones are not being exported", because studiomdl thinks these bones have no vertexes attached to them and cut them. The only ugly solution I found is to import your exported mesh into Milkshape3d and re-export it without bone weighting.

Animations should be exported fine AFAIK.

Binary 2 Model 1 works fine too (that's default one when you don't setup Engine Path)

Are you sure you used the latest version of BST? Cuz I had the similar issue, but it was fixed since some of the update released recently.

https://steamcommunity.com/sharedfiles/filedetails/?id=245723825

Grab readme.pdf from here:

https://github.com/revzin/HWMToolkit

Made a bugreport https://steamcommunity.com/groups/BlenderSourceTools/discussions/0/385429254942050851/

Directly references to this: https://steamcommunity.com/groups/BlenderSourceTools/discussions/1/385429254939812081/

Recently I was figuring out of why BST can't import his DMX. Here is what Blender outputs:
http://i.imgur.com/cz9RlI7.png

After converting it from binary format to text format, I noticed that it contains "broken" symbols after "user" "string":
https://imgur.com/4WPKUhs

So, I changed this into something else and re-converted it back to binary. After that, it succeeded to import!

Here are DMX files if interested, they are just animations: https://drive.google.com/file/d/0B-_fPt0ZqEtNNGJBWUNGWjNDalk/view?usp=sharing

DMX can be converted using dmxconvert. Here is the guide on how to use it:
https://steamcommunity.com/sharedfiles/filedetails/?id=551265085