Right, so that is a problem, but it's a different problem from lack of configurability. Those things are being addressed in other ways such as with the extension rebooted initiative: https://blogs.gnome.org/sri/2020/09/16/the-gnome-extensions-...
You're making a distinction of "third party" here but I don't understand why that really matters for configurability, for example it's no different from installing an unoffical XFCE panel applet, or using a third party file manager, etc. In the gnome shell, the extension API is built-in and standard. That is the configurability. If you're asking for specific panel settings to be included by default, that really isn't possible in a way that would please everyone -- you can look at the sheer number of panel extensions there are to see why that is the case. Again someone could make one to make it look and act exactly like XFCE's panel, but that would just be yet another option. Does that explain it? It's not really possible for the shell to act the way you're asking.
I support you using XFCE if that's what you want, but if you're asking for changes to be made in Gnome, those could probably not be made without causing much worse breakage. If you're not asking for that, then never mind, I misunderstood :)