Make the background separately from the title.
I'm trying this with a graphic, and I have footage below on a separate layer. Applying the Flip Over to the graphic on Video 2 track effects the video on V1 track. It IS separate.
i Think that you want it to look like a card is flipping and has a different graphic on the back. Unfortunately the flip transition forces there to be a solid color behind the flip which doesn’t look right. I would recommend the card wipe effect in After Effects.