None of our 23 cats wear, or will ever wear, collars. This is after two separate (with correctly fitted collars) incidents involving near strangulation. In the first case, the cat managed to get the collar trapped across the back of its neck and through its jaws. Fortunately, unlike most cats (who tend to hide when they have a problem) it cam and found me, and I was able to free it. In the second, we were alerted by crying, and found a cat hanging by its collar from a tree branch.
In our experience, cats that don't belong very rarely enter through a cat flap. I'd go with an ordinary, 3-way lockable flap.