Yes, but it's too complicated for me to explain by words and/or pictures.

Neither is best. DMX can have flexes built-in, with many options not available with SMD and VTA, but DMX is in Source limited to 3 bones trying to manipulate a vertice, and in Source 2 limited to 4 bones, while SMD is unlimited in that aspect.

But if you'd ask VALVe, they would say DMX if they'd reply.

It's supposed to make SMD, DMX and VTA files, however it does allow compiling QCs you make yourself. Personally, I prefer using cmd.exe to make StudioMDL compile models.

Or just don't use unusable physics models for Source FilmMaker...

In Garry's Mod? I don't know. In the model? Well, *shrug*, I don't work much with animations...

Which file contains the animations? That depends on what you set as $IncludeModel in the QC file.

Exactly why do you think Half-Life Model Viewer should view StudioModel Data?

Try replacing "man.smd" in the $Sequence thing with "man_ref.smd" or "anims/man.smd".

Then I don't know what's wrong, sorry.

Do you close your browser before extracting the archive?