Thanks, actually most of that is now clear to me.
Actually when working with two instances, I find the notification useful, what I wanted to avoid was the "overwrite" button, because I wanted to be sure to write to file from only one window.
I understand that geany permits running in multiple windows by running two separate processes with no communication or sharing of data structures.
But all considered it means what I'm trying to obtain cannot really be obtained except by adding to geany a multi-window functionality where two separate windows editing the same file actually share the same document/buffer.
I don't know geany source base well enough to judge but implementing that, while interesting, looks like a complex task that could take months.
So, at present I'll just close this pull request, maybe I'll think about something else to suggest in the future.