But the combination <Primary>Super_L/R can be set but does not work, nor does it do anything in the desktop, but maybe its still being stolen by it.

I guess so, it seems reasonable that the WM eats this combination and so it seems to not work.

But <primary><super>a can be set and works.

But the OP is getting <primary><super> which is two modifiers, @philiprbrenan @eht16 whats your Geany and GTK and OS and desktop version information?

That's true. No idea what's the difference.
I'm using Xfce 4.16 with
´´´
23:32:49: Geany INFO : Geany 1.38 (git >= b524a58), en_US.utf8
23:32:49: Geany INFO : GTK 3.24.29, GLib 2.68.2
23:32:49: Geany INFO : OS: Arch Linux
´´´

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