Yes the speed is the average speed over the points measured. It can be any distance less than 500m.
But note that because the Gybe is the slowest past of the track, the more straight line reaching you do at higher speed, the faster the average will be. So in practice, the fastest Alpha 500's will always be as close to 500m as possible.
If you calculate the Alpha 1000m and Alpha 250m from the same track segment, (assuming that you continued long enough to go 1000m at approximately the same speed), you will almost invariably find the Alpha 1000 faster and the Alpha 250 slower.
So I can say truthfully that I have done a 30 knot Alpha!

But it was an Alpha 1000!

For those who don't know, the speed of the Alpha is measured with the Doppler data, but the proximity circle is measured using the Locational data (trackpoint).
This is one of the reasons why Alpha speeds are not considered accurate enough for official records with the current technology. Better locational (and Doppler speed) accuracy from future GPS devices with higher hz data may change this.