Theme cannot be changed via GUI, system option missing
With 2573a9ed, it appears there's supposed to be 'system', 'light' and 'dark' theme options with 47.0, but there's only 'light' and 'dark`, so the theme is now light by default instead of matching the system theme and cannot be changed via the GUI. To set it to dark, I had to use GSettings:
gsettings set org.gnome.gedit.preferences.ui theme-variant 'dark'