It's an issue with flexible vertical spacing relating to ChordNames and
FretBoards, easily solved with setting this up with VerticalAxisGroup
alist property settings. Kevin sent me the score.
When I refine the solution I'll post something about it here soon.
I have to say, even after years of using LilyPond, I always find the
flexible vertical spacing settings manual page quite hard reading, I
suppose because there are so many fine details and interactions that can
be adjusted in all sorts of ways. But I could not think of a way to
write that section simpler of more clearly. It's just a subtle feature
of great power in LilyPond.
Andrew