After a bit of careful research in PyPRP's code, I found the core of our dreaded Region problem.
Befor I explain, you should know that the object that stores the physical info, is almost a direct copy of internal Havok Physics data, and thus has no relation to generic settings like coordinates and scale, that are set in other plasma objects.
Further, we have static physics objects (origin at 0,0,0 worldspace) used for generic collision, and dynamic physics objects (origin at objects center, and orientation set), used for kickables and most regions.
It turns out that the physics object has no concept of scale, but only center position and rotation. The PyPRP export by default didn't do anything with the vertices of dynamic physics objects, while it should have applied scale only.
Well, that's the story, I'm gonna try and fix it.