Create a rectangle, press ctrl+t, go to tool options, free, position, choose another measuring point than middle center and set position 0,0. You will see that it uses a middle center to measure the position and the rectangle will be half out of boundaries.
This happens with every measuring point, also with the every custom one (drag and drop measure point)

Reproducible: Always

Steps to Reproduce:
1. Create a rectangle
2. press ctrl+t
3. go to tool options
4. free
5. position
6. choose another measuring point than middle center
7. change position to 0,0

Actual Results:  
Wrong position