I don't see anything unusual in the CVs. Note that CV116 and 117 are not implemented in the Lenz decoder - it operates at a lower frequency than the NCE so it doesn't need torque compensation to run smoothly at low speeds.
All Atlas C420's came with scale speed motors, so with default decoder settings they will run slower at any given throttle position on your NCE PowerPro than a loco model with a higher speed motor and/or gearing.
Have you attempted to change the speed table CVs? If you're using the default decoder settings, comparing the loco speeds at a particular NCE PowerPro throttle position doesn't tell you much, other than that the locos have different voltage/speed characteristics. That's a locomotive, not decoder characteristic. You can't expect two different locos, even if they have the same decoders, to have the same throttle/speed profiles. To match loco throttle/speed profiles of two different locos, you need to change the speed table CVs of one or both of them.
For the Lenz you'll have to use the 28-step speed table (CVs 67-94), since the LE063XF has no CVs for the mid and top speeds when the minimum speed is controlled by CV2. For a 28-step speed table, CV94 determines the percent of the track voltage applied to the motor at the maximum throttle setting. For example, if CV94 = 100, the NCE PowerPro (or Digtrax, Lenz, etc control station) applies 100/255 = 39% track voltage at the highest throttle position (maximum CV value is 255). The CV67 value determines the percent of track voltage at the lowest throttle setting, e.g., with CV67=10, 3.9% of track voltage is applied at the lowest throttle position. I set the CV67 value at the lowest needed to get the loco to barely creep, and CV94 to get the maximum realistic prototypical speed, and then as a first approximation linearly interpolate the other speed table CVs between them. This can get done in a few minutes with JMRI DecoderPro. You'll also have to change the value of CV29 to 50 to activate the 28-step speed table.
Just replacing the LE063XF with TCS decoders will not automatically result in speed matching. You'll still have to go through the same process.