This "feature" is really extremely confusing. Every one of my customers has a question about it and wonders why the coupon code they created doesn't work. I really have that question every single time.
I mean, from a technical perspective, I fully understand the problem. The voucher code is entered at the checkout. And at this step it's not possible anymore to change the items in the cart, but from a user (store owner, as well as customer) perspective, this "automatic" discount isn't "automatic" at all.