Personally I agree, I think for the sake of simplicity it'd be better to just have people run on Ex 3. I played and submitted on vanilla since the current top time was played on it, so I assumed it was okay/expected.

As a little side note, you don't necessarily have to show the title screen, you can just show Amatsu on the stage select screen, which would confirm that the game is being played on Ex 3, and the timer doesn't start until you select the stage anyway. And the lack of the "arena" on the Doppelgänger fight as well as the completely different attack pattern on Baphomet would be dead giveaways as well (at least for vanilla, I'm not sure in which expansion those two particular changes were implemented).