The KP-xx keybindings are in the Scintilla editing widget, not Geany. That is documented [here](http://www.geany.org/manual/current/index.html#keyboard-commands).
In GTK any number of entities can bind to signals and Geany attempts to be the first on the list of signals for keyboard actions, so it gets first choice of actioning them, although other entities could override that. If Geany has a keybinding it performs it, and signals that the key is handled and so the signal is not delivered to any entities after Geany on the list. If Geany does not have a binding for the key it is passed to the next entity on the signals list, usually Scintilla, and so the Scintilla action happens. This is also how characters get inserted in the document as geany passes them to Scintilla.
The Scintilla keybindings are set in Scintilla and Geany has not been programmed to be able to change or remove them.
To date it has not been considered worthwhile adding that capability, but a well written pull request may be accepted if it has a reasonable UI or integrates into the Geany keybindings UI. As always with UIs be prepared for some discussion on that :)
The fact that Geany keybindings override snippet keybindings is documented [here](http://www.geany.org/manual/current/index.html#snippet-keybindings).
The Scintilla keyboard activating as well as the snippet looks at first sight to be a bug, #1354 added to track.