Well, Ramesses II offered to give the City at the end of the turn before the win was announced, but the player can't respond to the offer until the beginning of the next turn. The RL DV vote should not be tallied until the end of the turn in which the vote was solicited. It really should have included the Population of the gifted City, except it didn't have the TAP Religion in it any way.
I'm not entirely sure how the Score is computed, but my Score of 49987 was shown as part of the Win report screens, after I was offered the city by Ramesses II.
If you load the final save from submission #23557, you will see that the Score is 49987 and not 40529 as reported in my now accepted game. There appears to be a bug in the HOF software that accepts submissions, though certainly one that rarely raises its ugly head. By hovering over the player entry in the lower left corner, you will see that score from Population is based on 8 Population, but my capital can account for only 6 Pop, so it seems likely that the difference in score is the extra 2 Pop from the gifted city.
The HOF submission software claims my score is 40529, but that is obviously incorrect since the file I submitted has never reported any final score other than 49987 on my machine. I'm afraid the discrepancy in score is probably the result of a bug in the submission software which you may want to investigate. The final AutoSave includes the query of accepting the city offered and shows a Raw Score of 534 before accepting, but the file submitted was manually saved immediately after the win report screens and has a Raw Score of 586. Note that its not possible to hover over the Raw Score of 534 in the final turn (the victory screens intervene) before accepting the city, but if it were possible, it would likely show as 40529. However, BtS would never record this score as 40529, unless the player rejected the free city.
Would you like my final autosave so you can investigate? It might be interesting to see the score after rejecting the city offered.
Here is the autolog entries generated when accepting the city offered in the final autosave file:
Sun Tzu Wu