Atlas is awesome, but you have to watch their descriptions carefully. Some are 2 rail and many of the 3 rail come with Kadee style couplers only.
I have never seen a 3-rail car come directly from Atlas with anything other than 3-rail couplers. Have you gotten 3-rail cars with Kadees from Atlas?
Yes, when they are scale wheeled versions.
Are you sure you're not confusing them with the scale wheels versions that MTH offers in most of their Premier engine line? They're the only ones I know of that currently make "scale wheels" versions that work in either 3-rail or 2-rail and with 2-rail coupler mounts.
The only "scale wheels" engines that are 3-rail compatible by Atlas O that I'm aware of is as an aftermarket service that they offer for anyone that has bought Atlas O 3-rail engines and want them converted to scale wheels & Kadee couplers.
And having said all that, I have never, ever seen any freight cars from Atlas O, let alone MTH, that were 3-rail but with Kadee Couplers installed from the factory. Only thing I've seen is cars that were converted by a previous owner, or were 2-rail to begin with.
This was on rail cars not engines.