having not played many of these and recognising that everyone values different things (including play on the day) I wont opine on merits. Ialso havent read the article to see the criteria or number of raters etc, nor reasons why some werent ranked. But perhaps some observations in comparing the AGD and GA lists:
StAbeach ranked 14 places higher in GA than AGD (12 vs 26)
Gunamatta not ranked at all in AGD
Port Fairy ranked 26 places higher in GA than AGD (31 vs 57)
Concord ranked 14 places higher in GA than AGD (32 vs 46) - maybe AGD played the pre-reno version?
Portsea ranked 18 places higher in GA than AGD (34 vs 52)
Joondalup quarry/dunes 19 places lower GA than AGD (37 vs 18). Is Joondalup a top 20 course in Aus??
The Australian ranked 19 places lower on GA than AGD (40 vs 21) - is the Australian a top 25 course in Australia??
Eastern South ranked 39 places higher on GA than AGD (55 vs 94)
The Cut ranked 23 places lower on GA than AGD (59 vs 36)
Sanctuary Lakes ranked 30 places higher GA than AGD (60 vs 90)
Healsville ranked 25 places higher on GA than AGD (61 vs 86)
The two most glaring:
Ranfurlie not ranked at all on AGD, on GA its 60
West Australian not ranked at all on GA, on AGD its 56
The common theme in a lot of these seems to be GA ranks a lot of Victoria courses higher than AGD does. Some state based biases here one way or another?