The description of the run states: "(IGT is main timing method for this category)" does this mean the IGT determines rank?

Boss Battles uses RTA as the main timing method. Your place on the leaderboards would be determined by real time. The rules are incorrect.

That's a bit frustrating, and now it seems they have taken down that rule.

I guess me and my partner just feel a little robbed considering the rules stated we would be in 2nd place.

Theres not a way for me to make only Boss Battles IGT and not mess up the rest of the categories, otherwise IGT would be the main timing method for Boss Battles, just use it as a mental note that your time is better than me and Pokeheros haha