Correct, Atlas c55 flex track has larger spikes than either ME or Peco c55 track. That is why the flanges on the old MT "pizza cutter" wheels hit the spikes on Atlas track.
Also, in general models of European prototype have deeper flanges than US models. They also still use Rapido coupler as a standard coupler...
European modelers mostly use c80 track, so that deep flanges are not a problem. I also think that manufacturers aare still stuck with the notion that N sclse is a toy which needs deep flanges not to derail when going 300 scale miles per hour over uneven track or sharp curves.
I don't have any Atlas c55 flex track but I measured the flanges of some of my recently issued Brawa models.
A boxcar has flanges with depth of 0.76mm (0.030").
Another model locomotive has flanges with depth of 0.78mm (0.031") and yet another is 0.82mm (0.032").
For comparison, the troublesome "pizza cutters" have flanges depth of 0.89mm (0.035"). Older Kato loco's (P42) flanges are 0.75mm (0.029") and newer Katos are 0.54mm (0.021").
I would guess that the Brawa flanges are probably pretty close to hitting the spikes on Atlas c55 flex track.