@techee Ahh, your explanation above says no way of passing __ignored__ file patterns, I misread that as no way of passing any file patterns. So how do you pass them? By modifying the GStrv in the projects structure? If so I do hope thats intended to work, its not documented to work (or not) :)
So yeah, ok, the options are either upgrade Geany to support excluded patterns (would be nice) or as @codebrainz notes to allow setting the extra options or implement your own complete search capability.