Doors were added mainly because MCE built a house in the amethyst biome, and he didn't have any doors that went with the color scheme. So mauvewood was added and so were the doors, as well as the other wood stuff. Trapdoors were just apart of the wood stuff. The trapdoors from the mod work like any other normal door.
You can get secret trapdoors if you have the IDT mod installed, just ⇧ Shift right click with the chisel from that mod on a trapdoor.