I read that Beethoven had intended for the finale of Fidelio to start within 7 seconds of the last note of the Leonore and Florestan duet. A practice was begun to insert the Leonore #3 overture in between these two parts to accommodate the scene change (from dungeon to prison parade grounds). This I could understand in live performances, yet there are ways to cleverly make that scene change happen fast as in the DVD with Nylund and Kaufmann by having a curtain lift in the back of the dungeon scene exposing the new scene for the finale.
At any rate, I remove the Leonore #3 overture from all my folders before playing them on my MP3 player or burning discs for the car. I would remove the overture from the DVDs but it is probably not easy to do, so instead simply skip over the overture.
Leanora number three was played traditionally in opera houses to give time for the scene change between the dungeon scene and the finale which is set in the courtyard. Bernstein actually weaves it into the end of the duet. Works fine to me.