The date on my files is November 2008, so Abbey & Mayor was out for at least a year already by that time.
That the tournament is scored before a barn seems clear to me already in the following sentence: "When the game is over, the archery champion should always be scored prior to normal farm scoring."
Footnote 8 in Archery Tournament is essentially identical to Footnote 11 in Jousting Tournament, which was the inspiration for Archery Tournament. As the footnote states, such situations are very rare.
In fact, all of the rules in Archery Tournament are based on Jousting Tournament. I think the rules should remain consistent with each other, and since Joff is the original author I defer to his judgment on whether your suggestions are an improvement.