There could be unknown magic from the magic macguffin, which is just a reasonable as some connection to another universe. Something something friendship. Sunset can hate Sci Twi because Sci Twi is sweet and smart. There are plenty of people who hate other people for less than that. Her motivation would be power, just like a lot of villains. Perhaps she was corrupted by some evil magic.
My whole point is, the Pony connection was just an excuse, but the EG universe easily became its own thing. In fact, I think the pony connection detracts from EG. It's like, "oh yeah, I forgot that ponies exist in some other universe for some reason."