This is going to be a bit of a long response, so please bear with me.
Let me begin by saying that I have great respect for PowerTap products. They have gotten really good through the years, and I like their technology very much.
When I see differences between DFPM and our power meter data, I do a lot of checking to make sure that nothing in the rider's PM profile setup looks odd. In your case, all the weights, CdA and Crr coefficients look ok, and your wind data looks solid. I think your Newton is properly calibrated.
So, if there is a difference between DFPM and Newton readings (and there is a significant difference in this ride file), which power readings are to be trusted?
We don't know the details behind the way any DFPM calculates power--that is, we don't have the underlying torque measurements, temperatures, etc. That is not a criticism; it simply means that while we may know WHAT the DFPM power number is, we don't know HOW it was calculated. So, after-the-ride it isn't easy to validate the accuracy of the DFPM readings and calibration.
With Velocomp power data, it's different. Our ride file includes all the information used to make power calculations: bike speed, wind speed, slope, CdA, Crr. Why are these parameters useful after the ride? The only reason a cyclist must pedal a bike is because wind, hills, friction and acceleration oppose the forward motion of the bike. According to Newton's 3rd law, if those quantities are known, the amount of power used to climb a hill, ride on the flats, or any other combination of riding, can be calculated.
In fact, there is a website I use, "bikecalculator.com", that allows the user to input bike speed, hill slope, wind speed, ride position, and bike/rider weight, to estimate watts. So, in the Isaac ride file I can select any ride segment, get the bike speed/wind speed/slope/CdA/Crr and weight parameters for that section of the ride, and use the website to compute the watts. I can compare the bikecalculator.com watts calculation to the Newton/PowerPod watts number and PowerTap watts.
And I can pick various points in the ride file, to isolate the performance of our sensors and the rider's profile settings.
1) I try to find places in the ride file where the rider is riding on the flats at a constant speed. On the flats, wind speed dominates (if it is truly flat and the rider is traveling at a constant speed, then rider/bike weight is not a factor). If the Newton/PP watts are wrong, this would mean a problem with the wind sensor setting (wind scaling) or the CdA.
2) I find places in the ride file where there is a hill, to check accelerometer performance and rider/bike weight settings
3) I find places where the rider is on a gentle climb or descent, to check combined wind/accelerometer performance.
I go at least 10 minutes into a ride file, so that both Newton/PP and DFPM are stabilized.
And, to get "best" results from the bikecalculator.com site, I try to find ride segments where bike speed, hill slope, and wind speed are fairly constant (the website calculations assume these parameters don't vary; if they do then the calculations are less accurate).
With all of that as a preamble, what does this ride file show?
Overall, the data shows the PT on average to be 40W LOW. In fact, when looking in detail, the PT seems to be low almost everywhere. What's going on?
In the screen shots below, I input to bikecalculator.com the parameters of the ride segment I've selected. I show the Newton measurement for that section, and the PT measurement for that same section
1) Hill climb, time 1:12:30. Slope 3.31%, bike speed 10.1 mph, headwind 3.4 mph, rider weight 186 pounds. On hills, gravity watts dominate. If bike/rider weight is correct, then Newton watts should be solid. PT: 148.9, Newton reading: 182.8, bikecalculator: 189W. Newton is correct.
2) Flats. I picked a 1 min 42 segment around the 15 minute mark: 0.72% slope (pretty flat), bike speed 18.7 mph, wind speed -0.2 mph. In this section, wind force dominates. If wind speed and CdA are correct, then Newton watts should be solid. PT: 157.5W. Newton: 231.4W. Bikecalculator: 225W. Newton is correct.
3) Sprint. This is where both acceleration and wind are important. I picked the second sprint, around mile 12. Bike speed 24.2 mph, wind speed -0.9 mph, slope 0.57%. PT: 312W. Newton 368W, bikecalculator 375W. Newton is correct
In all of these sections (and everywhere else where I checked at random) the Newton was nearly identical to bikecalculator, and the PT reads low. How can this be? Well, all DFPMs require calibration prior to riding, and for best results they need to be re-zeroed during the ride. I have a PT wheel and when calibrated it works just fine. But I do find that calibrating it is a somewhat mysterious process, and that I some times think it is calibrated when, in fact, it is not. This is not a criticism; I am probably doing something improperly.
As a different kind of gut-check, I used Isaac to figure out the rider/bike weight and CdA that would cause the Newton readings to most closely replicate the PT measurements.
If the total bike/rider weight is lowered to 165 pounds (from 186), and the CdA is lowered from 0.33 (road bike) to 0.23 (TT bike), then the Newton very closely copies the PT result (within 5W). These are extreme adjustments that, in my opinion, are unreasonable to make.
Another way to "bludgeon" the Newton data to fit the PT is to lower the net wind speed. This drives down watts. I found that if the average wind speed for the ride was -3.5 mph, then the overall watts were close. But then, the ride file wind looks "funny" and doesn't seem possible. And note that, with this wind measurement adjustment, on the hills the Newton still reads high (accelerometer measurements dominate).
In sum, I don't find any reason to question the validity of the Newton measurements. I strongly suspect that the PT was out of calibration for this particular ride.
One final point: I did try the trick of using the "Check Calibration" correction on the Newton ride file, using the same profile. This trick certainly does bring the Newton close to the PT. Why? I have no clue. Isaac calculations are a mystery to me. However, there is no reason that the same profile information, applied to a ride, should modify the ride data. So, there appears to be a bug in Isaac.