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.