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I think you are missing a step between 7 and 8. You should Add a new Armature modifier (this is what attaches the vertex group weights back to the bones):
In Mesh's Modifier panel, select: Deform > Armature
Click the Object field.
Select the armature from the list.
The QC file has other bodygroups that come from different SMD files, so maybe the other SMDs that I haven't modified are causing the main SMD to get reverted?
It is definitely favourable for a model to either be built that way in the first place or not be used like that at all, especially considering the way a model is rigged and such (for example, you're saying the shoulders look "wrinkled" when in the same position as before).
If you really want to do it, you should do it by changing the pose of the SMD/DMX of the first $Sequence, while keeping the SMD(s)/DMX(es) used in $Model, $Body, and $BodyGroup un-altered.
And in any case, de-compiling a model isn't always flawless, and to be honest, it's rarely flawless when flexes are involved... and if it's a character, it likely has flexes, and if you're saying the model has shape keys when you import its QC or such through the Blender Source Tools, it definitely has flexes (which, again, usually doesn't de-compile that well).
TL;DR: If you are doing this only for the sake of a model by default starting with its arms in a different position, it's very far from worth it.
Could the other $BodyGroup entries be a problem, since they are all in the original Jesus pose?
If a bone is in a file used by a $Sequence, that bone will have the position and rotation it does in that $Sequence. If not, then the bone will have the position and rotation it does in the first referenced model file that has the bone in it. So if the modified-pose model is the one used first (in the first $Model/$Body/$BodyGroup), then the bones will have the modified pose unless un-modified bones of the same names are in a $Sequence. Something along those lines.
In other words, check the bones and their posing in the $Sequence file first of all.
There is a .vta file that has the same name as the main SMD, and seems to contain all the vertices used in all the SMDs. When I view those vertices in Blender none of them have the arms lowered, so could that be causing the pointy vertices in the modified model?