Yeh because it would be stupid that Superman has never been seen or even mentioned if the Arrow/Flash verse. Until the Flash the world at large seem to be unaware of any super power beings and Superman counts as SUPER hence the name. Keeping them separate in a different Earth separate from Earth 1 or 2 is the best way to go.
Earth 3?

Unless Earth 2's Central City is unique in it's stylings and technology, we haven't seen anything that would indicate Supergirl is on that world.
her world looks like too much like ours - even has Microsoft Surface tablets
