You shouldn’t need $upaxis at all really, it’s pretty much only when you’re exporting from Maya.
Maybe it doesn’t in this case, but there are times where the ragdoll sequence can differ from the mesh skeleton and break.
Plus it removes the need to keep track of that extra file. I personally prefer to do it, takes less than five seconds and saves a lot of hassle.
So like I said, it seems the only advice we can give in this case is “just rotate it to the correct direction”. Sorry.
EDIT: Wait a sec, is the problem the collision is not moving with the model, or it’s rotated relative to the whole thing? The first two images don’t show the phymodel.
If this is for Gmod, try spawning it and typing ‘vcollide_wireframe 1’ into the console.