Maybe this is really a difference of the old vrs new curve.
I notice that using the new curve Moonsingers Jason Score would have been 10467 instead of 11879. The new curve appears to make a significant difference in scoring based on victory type.
Overall it looks like the new curve penalizes the slower games more than then old one did.
I guess what this reallly boils down to is your definition of what the scoring system should measure.
Using the examples you used, I would consider Dave's win far more impressive, but Moonsinger's raw in-game score is enough that despite the 43 turn difference. (Admittedly they are different games so the comparison is not completely accurate)
If I set up a 3 way victory (say conquest, domination, cultural 20k) at 1700AD... should the score vary wildly based on which of the 3 I decide to go with? I played the same game either way, and IMO, it should score the same (or close to it) either way. I shouldn't be forced to finish one way due to the scoring system, and that's doubly important now that the Medal Play has been introduced, giving a specified target victory condition for each game.
I would say that the answer is yes. The mere fact that you could have done all three doesn't change the fact that you could have done your conquest or domination 50 turns earlier. To me this is the whole reason for having different base dates.
I would further argue that Medal Play should have nothing to do with GOTM scoring. They are different events. There is overlap in the games, but they shouldn't effect each other.
All that said I'm going to put one more example out there.
In GOTM 20
Culture 20K in 1555 with firaxis 3000 : 5389
Culture 20K in 1700 with firaxis 6000 : 5799
Who Played the better game? It is open to opinion but I would vote for the 1555 Win.
All this said. It all boils down to scoring and a decision appears to have been made that the scoring should reward expansion to the Domintaion limit. Fine, I don't agree, so I'll just play my games and not worry too much about what the score says.