I don't think I understand all details of your argumentation and especially not why it got that heated :(.
To me it seems, what the OP described is a valid scenario and it doesn't matter who is to blame as it just might happen to users (including me). So #4023 is a good countermeasure to just help users to get the panes back easily, even if it is not Geany's fault.
As I said in #4023, the sizes after the panes have been restored are not perfect on my system but they probably never will be perfect on all systems as it is certainly influcened by GTK themes and maybe DPIs and whatever else. So I think it is fine to restore it so somewhat sane sizes and so give the user the possibility to adjust to her needs.
Thanks @techee!