Interesting discussion in a way and I agree with other comments that the OP is a bit overthinking the shim issue - and maybe basing that overthinking on a misunderstanding of what's going on.
The comments about preferring a partial shim to get more original wood contact make no sense to me as the partial shim would pretty much ensure a "big" air gap in the neck pocket between the places where the neck makes contact with the body and the shim - so LESS contact overall. I guess that this is where the luthier's concerns on the ski jump come from as the neck bolts might pull the neck down to fill the gap, bending the end of the neck into a curve. I've seen that argued by several guitar builders/fixers... For example.
...is that true or not... no idea but it sort of
seems a bit plausible, sort of...
My personal preference based only on snake oil, mojo and an understanding of secondary school physics would push me towards a full pocket shim as that should maximise the wood on wood on wood contact area with vibrations being able to pass relatively unimpeded across the whole of the neck body joint and that
FEELS more logical to me than a neck joint where vibrations are being transferred across two separate areas with an air gap in between.
Photos from a similar Google search showing the difference between a partial and full pocket shim - for avoidance of doubt...
So on a personal basis (and as the above caveat says, on the basis of personal preference and presumption) my leaning would be to a full pocket shim - and I know many, many, many very well respected luthiers prefer to shim that way so it's by no means an "inferior" solution like the OP presumes (and of course a similar number happen to prefer a partial - no biggie!).
So, yes, we're definitely in the way overthinking it territory by the OP. So if the neck angle is now such that the magnets can be adjusted to stop magnetic interference and wolf tones I'd probably say that the OP should be pleased with a job well done and stop worrying about a "problem" which they seem to have invented in their own mind.