Yes...both full-length films are on the same WB "Boys Town" disc. (In fact, the sequel film has a longer running time than "Boys Town", per this box art below.)
Sounds like a great "Boys" deal....it's been on my To-Get list for some time now.
It's not the first time Warner has included another film as a bonus feature. When Dr. Jekyll and Mr. Hyde was released they included both the Fredric March and Spencer Tracy versions.
I wish they would do a re release of Showboat which included the Paul Robson/Irene Dunne(1936) version.
Side "A" has "Boys Town" while Side "B" has "Men of Boys Town". I haven't played the disc yet, but will do so after I watched "A Christmas Carol" and "Christmas in Connecticut" first.