They have constraints for applications like 2D game or other gameplay cases. When such constraint is applied you are accepting loss of the energy - if you constraint object to not move in Y axis any acceleration in this axis will be lost, which is not physically correct, but you might not care as you don’t want object to move in that direction at all.
Not sure what you mean by joints but physics constraints generate forces and use those forces to pull objects into place, they don’t override transforms of objects as that would be physically incorrect.
At the end of the day you can manually sweep all components and calculate their position from sweep results, you don’t have to simulate physics to “have physics”.