The 'Set Shortcut...' button is inside a GtkStack having only one column, not allowing to expand it.
I removed GtkStack keeping its 'Set Shortcut' child taking up two columns.
However, there is still a problem, when I have a shortcut registered and I add another one, but with the same combination, the message appears showing that there is already another one, so when resetting the Name, Command and Shortcut elements, they are indented.