…indeed this is somehow the crux of configurable GUI’s… sometimes you can configure until everthing is broken… and even if not the app has to write/read big conf files or store this all in the document… and the users complain about long loading times…
You can’t make blender to remember order or open / closed status of panels in this window (because it’s considered temporary window or some other technicality).
But you can prevent system / recent panels from showing up:
It seems that reordering of any GUI elements also doesn’t reflect with an additional star ( * ) in the Blender Preferences:Save Preferences button…
Anyway: I’m not a friend of this reordering by accident… (did this sometimes (and still) in Gimp until i recognized how to put an unfloated panel back… had to delete the config before i found out… because it would be saved instantly… still annoying ) this should be specificly enabled and saved in the Prefs…