Science does ignore things outside of the universe, but amazingly enough, everything that matters is, by definition, inside it.
In other words, suppose there is a soul. If we can still make a brain simulator that acts conscious, then it doesn't really matter, because it had no observable effect. If, because humans have souls and computers don't, we can't make a conscious brain simulator, then the soul has an observable effect, and can be reasoned about with science. Now, in the first case, you might say that the brain simulator acts conscious but isn't. It would be a lot like saying people with a different skin color act conscious but aren't, though - not morally defensible.
Religions are not dualist because their ability to reason without evidence has allowed them to see some great truth that science has missed. They're dualist because they were conceived before we came to the great realization that the behavior of living things emerges from the physical laws.