I think this is a very uncommon and special use case. I understand your intention but I'm not sure we should and are able to implement each possible use case in Geany. It is already pretty good customizable and extendable but we can't do everything.
Did you try the `save_config_on_file_change` as @elextr suggested? This is what changed to previous versions and disabling it will save the session only on quit and when the preferences dialog is closed, as it was before. Then you should get the previous behaviour.