Of course you get to decide how you use your tools, but Wilson does not recommend using them that way. Many of us do it the way that it turns out that they recommend. Stack the bullet onto the case, holding it so that your thumb and finger overlap the bullet and the case neck, and slide the die down over.
Ive done it both ways but havent done many with it yet.
Why dont they recommend it? I cant see a problem if your using boat tail bullets, now with flat base i could see some potential problems .