...I don't even know where to put that code, so I think it's best if I don't tinker with it. I'll try just deleting the flexes. (In the next release, will it then be possible to make a stationary flex of some kind, that could basically make the whole mesh use $compress/$stretch (in the material) as texture?)

Alright, so here I am, trying to make a more-bodygrouped (Hard-Ware Morph-flex) Spy, and I decide to make the cigarette bodygroupable. So I duplicate (shift+D) the head, name the object "cig", go to edit mode, and delete everything except the cigarette (as well as delete the cigarette of the normal head object). I set export type to DMX, set flex type to advanced, direct the flex controller block thing to spy_morphs_high.dmx from the Source SDK (the one I imported). I supress the spy_morphs_high group, export the head, and then I try to export the cigarette, but... http://sta.sh/022y4q99cbtb

Using Version 1.10.4 of the Blender Source Tools, in Blender 2.69, on a 64-bit Windows 7.

~Zwip-Zwap Zapony

If you need more help, just ask. (Thank you for telling me of that "implicit motionless bones" thing. I thought it by default was unchecked.)

The emotions and phonemes tab... I don't really know, but I think it would work to find tf_movies/models/player/hwm/scout_phoneme and _emotion.pre or something, and copy-paste them where you compiled the Aperture Concept Scout to (and rename if necessary, to [modelname]_[phoneme/emotion].pre).
And for the make him stand up part? Just import the hard-ware morph Scout again (with upaxis Z), export the head (after setting advanced flexes and such) (also with upaxis Z), and then use $upaxis y in the QC.
(The "$sequence ref" model/skeleton may need to be turned around -90 degrees on the X axis, or imported with upaxis Z, and exported with upaxis Y, in case that has upaxis Z.)

I do wonder, though... Why would StudioMDL support .smd (and .vta flexes for them) with >2 bone influence per vertice, when it doesn't support .dmx with >2 bone influence? It's stupid (and the only reason I'm unable to convert the pony models to .dmx) .

It seems that there are 2 vertices with >0 bone influence for 3 bones (spine3, neck, head). StudioMDL doesn't like that. However, the fact they have >2 bones now, but didn't usually have, is weird.

Just uncomment //upaxis Y (as the files have upaxis as Y, not Z), and it should compile, with him standing up when spawned. And I still have no idea what your problem might be, but as I have the latest version of the Source Tools, and it can compile for me, as well as I have Blender 2.69, I don't think it's just because you have a newer version of the Source Tools.

Edit: I hit the "Check for updates" button, it upgraded to version 1.10.3 (I had 1.10.2 before; forgot to update) of the Source Tools, and now I can't export the head. I'll mess around a little more tomorrow, and notify you all of the results.
Edit 2: I just derped, and set the flex controller block to the dmx folder instead of the morphs_high dmx file. Now it exported.
Edit 3:
"F:\SteamLibrary\SteamApps\common\SourceFilmmaker\game\bin\studiomdl.exe" -nop4 -r -game "F:\SteamLibrary\SteamApps\common\SourceFilmmaker\game\tf_movies" "F:\Blender\VZ Scout\scout.QC"
Process started >>>
WARNING: Environment Variable VMOD usermod and -game F:\SteamLibrary\SteamApps\common\SourceFilmmaker\game\tf_movies do not end with the same valueqdir: "f:\blender\vz scout\"
gamedir: "F:\SteamLibrary\SteamApps\common\SourceFilmmaker\game\tf_movies\"
g_path: "F:\Blender\VZ Scout\scout.QC"
Building binary model files...
Working on "scout.qc"
DMX Model f:\blender\vz scout\head=zero.dmx
ERROR: Too many bone influences per vertex!
ERROR: Aborted Processing on 'player/vz/scout.mdl'
<<< Process finished. (Exit code -1)
================ READY ================

...I meant the .dmx and such files, not .blend. :P (Textures unnecessary.)

Edit: Hard-Ware Morph Scout head that I have exported, and that works: http://sta.sh/01c80093jk4m

As it works just fine for me, I can try and send you the scout_morphs_high.dmx head I have if you want. However, I don't know what may be causing this bug (unless you went on about modifying the head in any way before exporting).
Hehe, I see you're trying to recompile the Concept Scout model (right?) or something into Hard-Ware Morph mode.

I have the latest version of the Blender Source Tools, however this bug does not happen for me. Can I have a look at the whole QC or something? And what studiomdl do you compile with?