The bond cell can be placed in different ways. You can do it with relative floorplanning with respect to the IO cell underneath it. You can also use a special command for this, I forget the name but it is something like placeBond or place_bond and it will try to do it for you. In the end, the responsability is still yours to make sure the bond aligns with the IO cell structure. If you get it wrong, you will get DRC violations. If you get it super wrong, you will get a floating bond and no DRC violations. Maybe ERC/LVS violations.