Most 2 rail trucks are made to NMRA recommendations which means the truck bolster sits a defined height above the rail. This is the case with the trucks made by mainly 2 rail mfgs. The NMRA recommendation also defines the height of the underbody of the floor above rail. the Body bolsters on cars made mainly by 2 rail mfgs are made to these specifications. Generally (there sometimes exceptions), you can replace the trucks from one mfg on a 2 rail car with trucks from another mfg and the couplers will still be right height and the car will look right.
The mfgs that do a mostly 3 rail business each make the truck height and body bolsters to fit their own couplers. First on all, the truck bolster is much higher and the body bolster is thinner. The trucks are designed to use specific couplers. While you can change trucks from one brand to another, it usually takes some work to get the car to sit right and look right.
As for changing wheels, I have converted quite a few 3 rail cars to 2 rail, and simply done that. Sometimes it is an easy fit. And often it is the easiest way to convert the car and get it to sit at the right height since the bolsters are designed to work with each other.
Up until the last few years, Atlas trucks were wide and required wheelsets with longer axles than most. the more recent releases are not like that. Easiest conversion is to use Atlas 2 rail wheelsets. Many MTH cars can use Athearn or Intermountain wheelsets. Some however require different axles. Most Lionel trucks require slightly longer axles than Athearn or MTH but the stamped metal truck bolsters can often be adjusted (bent) to accomodate these wheels.
It is fun and adventure to dig into some of these conversion projects. I have not done any passenger cars, so all my comments for conversion refer to freight cars. The NMRA recommendations however also apply to passenger.
