I agree, all weaver cars I am aware of are Scale size. the line did include a lower 40ft boxcar that is the size of the Atlas X29 car. I think they called it a "steel side" boxcar. This is a scale car based on a shorter height prototype than the PS-1 they did.
I don't know about MTH, but as said the PRemier ones I have converted to 2 rail have been scale size, but I have not done that many different kinds, The railking line may or may not be scale. Some of the older Premier releases with cast on detail were downgraded to Railking and are scale size. Many of the cars in the railking line are underszie for scale.
Atlas O trainman is scale with detail on about the same level as Weaver cast on. Different prototypes. Atlas does have a line that is more toy train size but I forget the name.
Pecos river Plastic boxcars are scale 50 ft cars. They are based on a large prototype car. Any of the traditional kit makers as far as I know made scale stuff only.
Lionel is the most confusing. You pretty much have to look at each model uniquely, there is no large group identification. One group that is scale and very nice is the "PS" series cars. There is a PS1 boxcar, PS5 Gondola, PS ? flatcar, and PS2 covered hopper. Lionel also did a 50 foot boxcar that is very nicely detailed and scale. I have seen it called "standard O" and by other names. One clue generally with Lionel is if the details such as grab irons, stirrups, roof walks, and brake rigging are listes as separate add-ons. Generally I have found cars with these features are scale cars. The recent GLA hoppers and Roundroof boxcars are scale size. Lionel also purchased the dies for the Weaver cars taht were made in the US. I think they call this the Lionscale line. These should all be scale if it only includes the previous Weaver releases.