The original Journal of Defense Management article is here:
http://www.omicsgroup.org/journals/g...74-1000144.pdf
Note the line, "The current problem is focused on purely beyond visual range air-to-air combat missions".
As far as I can tell, Colonel Lee's background is in GCI and AWACS. The various articles mentioned that he has "trained
with thousands of fighter pilots", and "flown
in a number of fighter aircraft". (My italics)
None of which is to denigrate the achievements of either the ALPHA team or Colonel Lee, but having someone who isn't a qualified pilot (however tactically knowledgeable) flying a BVR simulation is obviously very different to an experienced fighter pilot being defeated by AI in WVR ACM.
The "Computer Beats Top Gun in Dogfights" headlines are BS - at least for now.