Yep, you have to cut that piece out to make a little more room for the GT40 transmission, and a section of the spare tire well needs to be cut so that the rear end can't rub against it when the suspension is under full compression (accelerating) You lose access to your spare tire anyways because of the fuel cell so it's a minor thing.
All of the stock trim pieces, like the center console, go right back in place after the conversion though. Nobody would be able to tell you ever made a cut.
