Mike and All,
I used Peco track on other layouts. The only trouble I had with flanges was on the older Rivarossi steamers and this only occurred at the Peco turnout frogs. My "Pizza Cutter" MT wheels never hit the spikes either. I switched to Atlas track just because of the cost.
On this layout it is interesting to note that the Peco On30 track, which is really code 100 HO rail translated to code 80 in O scale, is not recessed into the ties at all. If it weren't for the correct tie spacing which the Peco has and the Atlas does not, I would be using the Atlas flex this time too. And true to form, the flanges on the C-16s, Shay and all the cars which are RP25, low profile contour, do not bump at the frog of the Peco turnouts.
I'm not sure about deep flanges in N scale and Atlas turnouts, but I have had the experience of frog bumping with the Peco code 80 turnouts.
B-)