It's probably worth mentioning, 2D and some 3D operations rely solely on user entered heights, and it's up to the user to decide what has/hasn't already been machined, and set heights accordingly.

Some 3D operations give the option of REST machining, whereby Fusion will base the toolpath of remaining material, not the original stock, and will handle heights automatically within the tolerances set.

It all depends on what you're trying to achieve. Basic 2D is better for some stuff, 3D is essential for some stuff, some stuff 3D makes life a bit easier/better (I.e. adaptive and trochoidal), and some stuff 3D just overly complicates things for no/marginal gain.