Welcome to Geof and Welcome Jon,
This reply is geared towards Jon's request for feedback
Hi Jon,
You have several options, I feel.
1) You could do nothing, assuming you are not also seeing a number of feeder roots exposed on the surface (or above it), the trees on B118 and MM111 should adapt just fine
2) You could add soil to each tree to mound them up 2-3 inches each
3) You could add 3-4 inches of pea gravel mulch to each tree as it will benefit your plantings on several fronts
The drama of the higher (too high) planting will diminish over time as your trees grow and will ultimately be negligible.
On MM111, I have had noted problems with excessive burr knotting on varieties that were planted higher out of the ground then others. This has not been an across the board problem though. It definitely varied by cultivar. This may be in part why Penn State wants the grant to be just barely above the soil line for MM111.
As you said, "6 inches on average" that means to me that some are still 8 or 9 inches above grade? That is too much in my opinion. I would add soil to those trees and gently taper it to the native soil line in a ~4ft diameter circle around the trees. Mulch as needed to protect that area and keep the soil there (lest it potentially erode away)
If it were me, I would do a combination of #2 and #3 above. Depending on my soil testing results, I would also take advantage of the opportunity to then use the native soil and blend in some key amendments (rock dusts, any meals, humates, etc.) and top dress those trees as desired, as the young trees will be feeding in that area in the next few seasons anyway, then pea gravel mulch a 3-4ft ring around each tree and ramial wood mulch the area just beyond that. 30 trees and this kind of work plan is very doable over a day or two.
The soil settling aspect varies from site to site, soil type, slope, how holes were prepared, management practices, and more will all play into the net results. You have had most of a full season in the ground with these trees . . . What kind of settling did you see occur in your planting?
Jon and Geof, post up some photos too, those are always nice to see along with the story at hand.
Gopher Hill ApplesZone 8 in California