Hey…It just depends on the transition between individual shapes. When you intersect two separate meshes, there will be a sharp angle where they intersect, and since the parts are not connected, you cant bevel it or make it smoother.
So, if we take the eye example, there is a sharp angle between the eye and eyelid in real life, because they are obviously two separate pieces, so it makes sense to have the eye separate.
The lips are connected to face so it would look weird if they were a separate mesh.
Also, even when two parts of your model are connected in real life, if you never see the transition, you dont have to model it as one mesh. For example, the tongue. It is connected to the inside of the mouth, but if you never actually see the connection, you can make it separate.
