I didn't think I needed to go into detail on bones/rigging/animating. General answers are quicker and get the point across without a lot of exposition.
1. Bones/rigging/animating is the general answer. To avoid clipping every model should be precisely the same proportion and bone structure it's the only way if animator wants to use the same animation sequence over and over again and avoid clipping. It is not my fantasies it's a fact, ask any 3d animator if you don't believe me.
2. Game has physics, you can see it every time then enemy body flying around and fall to the ground this is physics, however it's not nvidia physics, praise the maker. Another example about using the same animation, there is a cutscene then your character talks to Cassandra about chantry and then they approaching to the window and your character leans against the wall. If it is big male character it looks ok, but if your character let's say female elf, it looks like she leans against the empty space, you can see huge gap between her spine and wall. You know why? Because they used the same animation sequence and it was created for much bigger 3d model. And you know the funniest thing? It's very easy to correct they just do not care.