If I had to take a guess, the battery tracking apps are comparing current charge capacity to the original factory maximum the device delivered with, but Apple is comparing to some (lower) artificial capacity that they’ve picked as normal for the device.
From this page on interpreting the analytics file:
I suspect most of the utilities are using the MaximumFCC figure and giving a percentage of that, but Apple is using something more like the rated capacity instead.
That would explain their consistently higher health numbers, since (article’s use of average notwithstanding) the actual delivered capacity generally equals or exceeds the rated one.