>>evolution doesn't encapsulate.

I'm not a biologist or geneticists but from everything that I've read about cellular biology and genetics I get the strong feeling that there is a lot of encapsulation going on. Sure, it isn't 100% percent perfect but there is still encapsulation going on. Evolution would probably be way harder without it.

One hint is the human body, there are lots of encapsulations: eyes, heart, kidneys, digestive system, etc.

Evolution can repurpose an existing system for a completely different use with just some tweaking.