It's not that special of a case. Hiding a staff containing notes and using a MarkLine are normal techniques for managing a large ensemble score.
markLengthOn = {
\override Score.MetronomeMark.extra-spacing-width = #'(0 . 1.0)
\override Score.RehearsalMark.extra-spacing-width = #'(-0.5 . 0.5)
% Raise as much as four staff-spaces before pushing notecolumns right
\override Score.MetronomeMark.extra-spacing-height = #'(4 . 4)
\override Score.RehearsalMark.extra-spacing-height = #'(4 . 4)
}
So it appears the relevant difference is setting some positive extra-spacing-height when setting extra-spacing-width. On further testing with ledger lines and placing a staff above the MarkLine, the right setting seems to be MetronomeMark.extra-spacing-height = #'(4 . 0), rather than #'(4 . 4).
I still wonder if there is a bug in the interaction with hidden staves. Staves shouldn't be affecting spacing on systems where they are dead.