The "special fare" designation on the fares through AA Vacations is orthogonal to the price paid for AA Vacations fares. One will almost always pay less through AA Vacations for the same flights. It may, or may not, have the "Special fare" designator (*). So, one can get both the lower price and a non-special fare.
I don't think this is correct. When I price out trips that don't show special fares on either leg, the prices are essentially identical to what I see on Matrix/aa.com. Can you given an example of flights where this is not the case?