I saw that question on Yahoo, and thought readers here might also be interested in the answer:
First the politics: There are extremists among trans activists who oppose the very idea of autogynephilia, despite all the scientific evidence for it. They believe that it makes their desire to live as female less genuine, and they attack (sometimes quite viciously) anyone who endorses the idea.
Now, for the actual distinction between autogynephilia and being a transwoman: Autogynephilia is when someone born male experiences sexual arousal to the image of being female. Some people express their autogynephilia through cross-dressing, and some people express it only during sexual arousal and masturbation. Some people express it through clothes and relatively visible means, and some people want to express it permanently and opt for genital surgery in addition to whatever cosmetic changes help them be perceived as female.
Autogynephilia is not the only thing that can motivate a bio male to want to live as female. The other can be thought of as extreme homosexuality...sort of like gay men who are so gay, they are actually happier living as female. These are the folks who were very obviously feminine boys during childhood, unlike the autogynephiles, who were unremarkably masculine boys in childhood.
So, that's the difference: Autogynephilia is a desire that can motivate (some) bio males to want to live as female, and trans women are those who are living as female (regardless of what motivated them).
Unfortunately, the internalized autogynephobia in the trans community has made it nearly impossible for people to come out as autogynephilic, even within their own communities and to other autogynephiles. As a political movement, activists do not want to be recognized as living as women; they will accept only those ideas that validate that they actually were women all along. It's understandable politically, but not accurate, scientifically.