Hi Michiel,
Not an answer to your direct question, but closely related. Have you considered using set-global-staff-size?
From the NR Section 4.2.2. [version 2.19.59]
To set the staff size globally for all scores in a file (or in a \book block, to be precise), use set-global-staff-size:
#(set-global-staff-size 14)
The above example sets the global default staff size to 14pt (4.92mm) and scales all fonts accordingly.
Works for me.
The NR tends to suggest \magnifyStaff is mostly used for setting the staff size for a single staff in a system.