HLFRITZ,
What scale size (length, width or height) should be for a passenger car depends on the railroad you are modeling and the manufacturer of the cars used by that railroad. The height factor is usually limited by clearances (tunnels, station overhangs, etc.) that already exist when the railroad ordered the cars. Most modelers are more concerned about length because that factor determines the minimum acceptable track radius to be used successfully with the cars.
If you desire to model a certain railroad, search the internet for info about that railroad's passenger cars and car suppliers. While I'm not positive about this, I will offer my opinion that Madison cars were not made to "scale" because no real Madison cars existed. I believe they were made to be "representations" of real heavyweight passenger cars that would travel through model curves.
You seem to focus on the height. I would suggest you take the engine you might be pulling these cars with and measure it on the tracks. Then, compare that to your known 12" height of the cars you like. If you're satisfied, move forward. If not, look around for something else that suits your fancy.
Chuck