Bob, you are correct about the flange. Matt did mention it in his post.
"This also means that the flanges on scale wheels are farther out than on a hi-rail wheel."
Same meaning just a different way of saying it.
I noticed that the flanges were not the same on 2 rail and 3 rail equipment when I tried to build a display case that would have grooves for the flanges. I wasn't easy but eventually I found a happy medium that worked with both types.
I have a board around somewhere I cut grooves in for painting purposes and I made double cuts with the table saw to widen the grooves to handle hi-rail wheelsets. The reason the scale wheelsets have a wider "back gauge" is simply because the wheels are substantially narrower and in compliance with the flangeway specs under RP25. Hi-rail wheels by virtue of their overall thickness and the flange size/countour have a tighter back gauge which is what makes them incompatible with standard 2-rail turnout guard rails and flangeways.
By the way, one of the best tools I have is a Kadee Coupler height gauge which has a flange checker, a height gauge, a trip pin gauge, and can give you a good idea of whether your track is in gauge.