https://factorio.com/blog/post/fff-133 explains what is going and why the existing graphics confirm to the official convention.
I've talked to Yuokitani and others about it. We tried different ways of lengthening the sprites when they go vertical but they all look really weird.
In a normal perspective world, you would not be able to see the vestibule door on the end of the car if there was another car coupled to it. You'll notice the "extension" on the normal wagon sprite is just the fact that the roof covers the now-larger gap behind it. A flatcar has no roof so the gap is uncovered.
I.e. the wheels under the wagon are still in the same place as they are in a vanilla wagon. If there was a better way I would use it.