The subD is happening "in the pipe" The base mash is always being processed before it renders, even in preview. If the mesh gets baked at any point it actually changes the behavior of the mesh in joints. And not in a good way.

Vertexes are welded in the base before the subD. That shouldn't be affected.

That comparison mesh is a little disturbing. The only thing I can think of that makes even a grain of sense is the inherent inaccuracy of floating point operations. And that may explain the exploding mesh too. The inaccuracy adds up and at some point cause the resultant mesh to be malformed in someway. Perhaps 2 vertexes converge.

That also makes it really hard to reproduce but if it is actually the cause increasing the precision of that calculation may help. Basically add a couple of relevant digits to the math like was done to all the posing in 11 to combat "left side asymmetry" in figures.