Simulink 3D Animation requires you to simulate the robot dynamics separately, and then whatever positions you get from your simulation you apply to the virtual world. The advantage is that this toolbox lets you position other objects in the world and simulate sensors like cameras, lidars, etc.
Mechanics Explorer is the visualization for Simscape Multibody, which models the full dynamics of your system. But it does not have virtual sensor models. If all you need is the physics of the arm and its actuators, and no perception, this is probably better.
Technically, you can simulate the dynamics with Simscape Multibody, (optionally) turn off the Mechanics Explorer, and input the resulting body/joint positions in a Simulink 3D Animation world.