Hi @Ross,
the quantification value is only applied automatically when the xml product is open. When opening the jp2 image, the metadata (which is present in the xml file) is ignored and no scale factors are used.
The difference between the images should be just the quantification value, but for that, it is necessary to compare the pixel values at the same image level (in SNAP different level of the image are used depending on the zoom).
You can see the level in the lower right corner of the window:
It is possible to check if the pixel values are the same or not by using band maths tool. You can create a new band with the expression:
NewBand = round(Band1FromXML*10000 - Band1FromJP2)
where 10000 is the quantification value and the round operator is used to avoid rounding effects (if you do not use it, you will obtain errors of 0.000X instead of zero).
Please, could you confirm that the reason for the differences is the multilevel image? If not, could you please explain me what product are you using to examine it in detail?
Regards,
Omar.