Since we use the rigid body transform when transforming rigid bodies
things like parents and constraints add an offset because rigid body
transforms are in global space.
Now we just don't take rigid body transform into account on simulation
start frame so there are no problems when doing the initial setup.
The problem still exists when simulation is running of course.
To properly fix this we'd have to solve parenting and constratins while
taking rigid bodies into account before and after transform.
We'll have to see if it's really needed, would like to avoid it though.