@rsramkis please supply the version of GTK you used for this and confirm all applications are using Wayland, not XWayland.
IIUC (1) (a) (b) (2) (a) (b) have nothing to do with Geany, somebody else's problem :-) but they seem to indicate that middle click doesn't work for any applications, so should be reported to GTK if you are using latest (3.24.36)