Thanks for your response,
I think my problem is some kind of bug in USD… in the meantime I had a deeper look into it, and have created a very small scene to reproduce the problem under my original post ( Possible Bug: BoundingBox for prims with geometries with skeleton animation are to large - Omniverse / Developer - NVIDIA Developer Forums)
It looks like USD does not calculate the bounds correct for meshes with skeleton animations in some scenarios…