Is it me or are there differences between MTH premier, Atlas ,Williams, Weaver, Crown scale rolling stock?
Yes, there are many differences in level of detail, quality of decoration and scale fidelity.
Williams cars are "traditional" toy trains. That means their scale is anything the manufacturer wants it to be.
Atlas also makes traditional toy trains from the former industrial rail product line. The decoration is wonderful and details like car dimensions or capacities may be accurate to the prototype even if the model is not scale sized.
Atlas trainman, atlas masterline and MTH premier cars are scale models as is the Lionel Standard O line and Weaver models.
Weaver has recently introduced scale modes of some distinctive freight cars from the late 1930s. These are dimensionally accurate and well detailed. Some of the older Weaver tooling is far less detailed and may be based on somewhat uncertain prototypes. Decoration may or may not reflect accurate dimensions, especially on these older cars. The Weaver "steel sided" and single sheathed box cars are from old tooling and based on smaller prototypes from the 1920s or early 1930s.
In the real world tank cars come in a wide variety of sizes based on the products that they are designed to haul. Sulfuric Acid weighs about 15 pounds per gallon while ethanol weighs about 6 1/2. So acid tank cars are quite small in volumetric capacity while ethanol tank cars are very large.
Covered hopper are like tank cars in that they are used to haul different commodities. A cement hopper doesn't need hold more than a few thousand cubic feet to reach it's maximum allowed weight wile one designed for plastic pellets will be over 5000 cubic feet.
There are about 40 O scale models of box cars available today. Some are based on 40 ton cars from the world war one era. Some are models of 1990s prototypes. And there are several dozen models based on prototypes from the decades in between. Freight cars became much, much larger over the 20th century and our scale models reflect that.