It reads like the AP is doing noise averaging (to reduce the noise) during the linearity sweep (?)
APx555 out of box has a simple linearity measurement with no filtering but only goes as deep as -65 dB. Here is the graph by default:
As you see it goes from -60 dB to +5 for a total of 65 dB from zero reference. In this use, no filtering or noise reduction is necessary as they are well below what the template was designed for.
The moment you dial this way down to -120 or heaven forbid, -140 dB, you are on your own to figure out how to create correct measurements.
APx555 provides a number of canned filters with different responses that can be used including a full custom one which is what I have created. Either way, the measurements are in the domain of what the operator does than what AP provided.
For my older AP SY2522 analyzer, Audio Precision provided the full solution in the form of cascaded digital and analog analyzers with bandpass filtering. That was nice because we could all use and follow the same script and there was nothing left to interpretation/setup.
The scheme for getting rid of offset was also different in that the older AP would try to use a least error method to use as a reference whereas the new APx555 uses that -20 db (or whatever you set) as reference.
Finally, for ALL measurements in AP, behind the scenes there is a settling algorithm that attempts to make sense out of run to run variations. The older analyzer had the same but due to differences in underlying measurements, I find that the APx555 gives up on finding the optimal value when the measurement values are small (whether it is THD, IMD, or simple amplitude measurements). We are dealing with very small values in our testing of DACs which apparently is not a common scenario. Fortunately the parameters can and should be adjusted for values to converge.
This is the reason I say that the claim that APx555 is better than 2522 and hence anything it shows is more accurate then 2522 just doesn't hold. If you want to compare those sets of measurements you need to set up the APx555 so that it closely emulates what the 2522 did. Otherwise you have two different measurements.