Cufflux#1979 の投稿を引用：

That would be a quick fix to this issue.

Yeah... of course, except if it was to be done for all vertices of a >10000-triangle mesh (thus with >30000 vertices) upon an import.

Blender fully supports custom normals, as seen when importing DMX files or importing SMD files with "preserve normals" or whatever it's labelled as checked.
However, due to the nature of Blender not liking to merge vertices with custom normals, and SMDs consisting entirely of separate triangles (unlike DMX), you can't both have custom normals on imported SMDs and have the vertices of SMDs welded together, with the default being to weld the vertices.

...Okay then. My bad. Continue on with this bug report, then.

For the weird rotations... You realize the source DMX files included with the Source SDK have different rotations than when compiled into an MDL, right? As such, it's also different for the animations.

For the bones, Team Fortress 2 has things like prop_bone, weapon_targe, heck, even weapon_bone, that the DMX sources don't (compiled into the model using $DefineBone to define bones the mesh doesn't have).

Thus, neither of these are a bug with the Blender Source Tools.

From part of the Studiomdl Data page on the VALVe Developer Wiki:

<int|Parent bone> <float|PosX PosY PosZ> <normal|NormX NormY NormZ> <normal|U V> <int|links> <int|Bone ID> <normal|Weight> [...]
-
The final three values are optional: they override <Parent bone> to define a series of weightmap links.

As you can see, the first value doesn't (necessarily) correspond to the bone that affects the model.
Regardless, could you please point out what the error is in the "compiled model" screenshot?

Decompile the model (the one with the animations) using Crowbar, then import one of the animation SMDs in Blender after importing a mesh and such. (Note that Crowbar might not like animations from some MDL versions.)

AlexH898 の投稿を引用：

I see you a little bit of everywhere helping people. Be it - Gamebanana.

Well, good to know people recognize me across different sites.

You have to extract the used VTFs, turn them into PNGs or something, and manually load those in Blender. The Blender Source Tools don't load VTFs (nor VMTs), nor any other sort of material or texture files.

jario_362 の投稿を引用：

is it ok if I credit you

Sure, I guess.

Yes, lots of stuff. (But nothing which I want.)