Here at Bandimere, home of the Mile High Nationals, they definitely check for a master cutoff switch if the battery has been relocated to the trunk. What's more, they also check for functionality. They let me run anyhow since my car's only in the 13's, but I was told to get it fixed before next time.
The "proper" way to do it is to run the alternator wire all the way back to the battery side of the cutoff switch; otherwise, the alternator will supply enough juice to keep the car running when the battery is disconnected. I knew this beforehand, but ran out of time before my first track day of the season.
So much for saving weight with my gel cell...