General rule is newer settings hold precedence.(posted 8903 days ago)However, there was a rule change that I started to introduce where the top 3 players could vote on making a game TG settings only. I don't think this ever went to vote (I think it is posted under 'illegal recordings' somewhere)
The easiest solution for this game would be to have players play at the TG settings, and make those the settings for the game (as we did for Bombjack and Joust, which, incidentally, do not yet have a Special Rules link attached to them to mention this fact) and then you don't have to worry about settings cahanges between versions.