I don't suppose there is any chance you can test with GTK3 Geany on Windows?
It does work with GTK+3 on Windows:
<img width="637" alt="geany_ligatures_gtk3_win32" src="https://user-images.githubusercontent.com/181177/91111750-2d3fcd80-e636-11ea-9ce4-f88807b2dab8.png">