Gnome has another set of hidden settings to set default system font sizes: for UI elements and "document" font. Some non-GNOME apps used to respect that too (like Firefox and LibreOffice), but others were not-scaled.
Still, if you mostly relied on Gtk+ apps, where Gtk+ widgets scale to fit the text they are showing, this produced pretty good results even if some spacing was a bit inconsistent (i.e. spacing was too small compared to widget and text sizes).
Unfortunately, this approach seems to work less and less well as Gnome devs are following Apple's lead.
Still, if you mostly relied on Gtk+ apps, where Gtk+ widgets scale to fit the text they are showing, this produced pretty good results even if some spacing was a bit inconsistent (i.e. spacing was too small compared to widget and text sizes).
Unfortunately, this approach seems to work less and less well as Gnome devs are following Apple's lead.