(I tried Keybindings, but pressing Esc closes the dialog that records the shortcut).

Yes, the GTK toolkit hijacks esc as the close dialog key, happens on any dialog, not just the keybinding one.

Possibly not a good key to use for that reason.

Just out of interest why do you need to keep closing Geany? It should open new files in the existing instance if one is running, so you only need to close the tab.

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