I don't think understanding emotions would be too difficult, they don't have to have any emotions themselves to understand how emotions work in people... And maybe they would not even want to live with people, nobody is stopping them from moving somewhere where there is no people XD

>>>the villains themselves were once naive and were betrayed and now not willing to trust anymore.
I think that is often the backstory of villains, usually there is some reason why they have turned evil. I don't know how realistic it is because I feel that sometimes evil people can just be evil without any deep sad reason in their past, but at least a reason is somehow more satisfying for the viewers because people usually look for reasons why things happen, it is in human nature to look for logical connections.

In the end, fanfiction exists for fun, so people should have fun with it!