Logging out/closing all my programs and logging back in applied the theming after all.
The GTK API reference for GtkCssProvider (the unstable dev version - I cant find the equivalent sections for stable) explains/confirms how GTK will read CSS code for a theme on startup:
An application can cause GTK+ to parse a specific CSS style sheet by calling gtk_css_provider_load_from_file() and adding the provider with gtk_style_context_add_provider() or gtk_style_context_add_provider_for_screen().
In addition, certain files will be read when GTK+ is initialized. First, the file $XDG_CONFIG_HOME/gtk-3.0/gtk.css is loaded if it exists.
Then, GTK+ tries to load $HOME/.themes/theme-name/gtk-3.0/gtk.css, falling back to datadir/share/themes/theme-name/gtk-3.0/gtk.css, where theme-name is the name of the current theme (see the "gtk-theme-name" setting) and datadir is the prefix configured when GTK+ was compiled, unless overridden by the GTK_DATA_PREFIX environment variable.
Previous experience suggested gnome-terminal all you needed to do was close all gnome-terminal tabs and windows to make new theming take effect.
As per the docs, maybe GTK needed to go through its initialisation, or there may have been a
gnome-terminal process still running, requiring me to logout and back in.