Okay, as it turns out, the exported DMX of the reference pose from SFM (and imported into Blender) uses some kind of local transforms for the poses, relative to the parent bone (leg to hip for example), while Blender defaults them at zero rotation and zero location. Or something like that. Either way, basically you export the reference pose from SFM as a DMX, you import it into Blender, then you either modify it there, or use a pre-existing animation of another skeleton (careful when importing the .dmx or .smd, you can choose new skeleton, append to current etc) to basically snap the imported DMX to the skeleton you already animated in Blender. Complicated, but certainly not impossible. There are such addons out there, such as the Blender Retarget Tool. Honestly it's easier to just animate in Blender and render with Eevee, but that doesn't work for maps, etc. Eevee is way faster than SFM anyway

Could you perhaps try exporting an animation from Blender into Source Filmmaker, and see if it works? Could it be my Blender version? I really don't know, do you have any other advice?

Yes, I just tried recompiling a separate, non-HWM model, a Heavy model, and again, same thing. The bones' outline looks good in SFM, but the model's arms and legs are distorted when importing a custom animation from Blender

Originally posted by Artfunkel:

Are you exporting your animations with the same up axis as the reference mesh?

Thank you for answering! Yes, the same axis as the reference mesh, as the skeleton, as the scene, as the import settings, yes.

Hello, I have a very serious issue, the exported (With the latest version from GitHub of the Blender Source Engine Addon) animations from Blender (animated on a TF2 skeleton extracted with the latest version of Crowbar, models from the SFM folders) do not work as expected inside SFM. They look somehow rotated and scaled. The format I have used is .DMX, since I try to import the animation directly from Blender to SFM. I have tried everything: different armature settings, applying all the transforms, nothing has worked so far. It appears to be an issue with the plugin itself, as other animations which work inside SFM do not work when imported into Blender, so an issue with SFM, Crowbar, or Blender is out of the question. (Do not work when imported into Blender, as in the same glitches with scaling and rotation appear). The skeleton itself appears to be correctly positioned, though. Reattaching to the model doesn't work. The head and torso (spine) parts are the only ones that work correctly. I did not edit the armature, only posed it and keyframed it. I suspect it has something to do with the 3D axis in Source (Y for height) vs the ones in Blender (Z for height). If someone thinks of a solution, please, help me out. Thank you. Here are a few screenshots showcasing the glitches
https://imgur.com/a/7fVHqPH