Yes, the Atlas model has two hinges per door. And the Atlas HO model is of an entirely different car, with different details. Nor is it a model of a Swift reefer, Atlas claims it is a model of a Cudahy reefer built in 1925 by General American. I have a photo of a Cudahy reefer built in 1928 that looks very very close to the Atlas model. The Rapido meat reefer is a reefer built by General American between 1937 -1941. Rapido used prototype documents, drawings etc to get their model correct. It is a different design from the Atlas model. Both are legit steam era meat reefers and we HO modelers of meat traffic are grateful for both models.

To my knowledge there was no rule that required three hinges per door. Many reefers were built with two hinges per door. Look at the many doors in your house and I suspect you will find some have three hinges and others have two hinges. The main reasons are 1) the weight of the door, ie its design and 2) the function of the door. A closet door with a skin is not an main entry door made of solid wood, steel or fiberglass. Reefer designs varied and different manufactures had different ideas and buyers had different demands.