I have found no logical difference in journals between scale and 3-rail wheelsets. All the Atlas ones I have dealt with have the same axles, whether 2 or 3 rail. I have pulled the 3 rail wheels from some of the axles and replaced them with 2 rail wheels.
On most of the Lionel stuff I have converted, the 3 rail axles have larger journals than the 2 rail ones I used. On some MTH cars, they have gone both ways.
I generally use needle point axles these days and they roll better. Older Walthers and scalecraft may have larger diameter axles.