Disclaimer: This is just my personal view on this, based on GNOME’s design principles, but any opinions here are only my own.
The hidden settings you can change with GNOME Tweaks or Refine are often there out of historical reasons or to allow for testing, etc…
Adding any one of these to the GNOME Control Center means that GNOME officially commits to supporting this preference for any user of GNOME. This means not only adding it, but supporting and maintaining it for the foreseeable time.
And any preferences comes with additional costs in maintenance. See also “Choosing our preferences”.
I will comment on the specific points you’ve mentioned, but as a general point:
Making an preference in Tweaks official in the control center needs to be done with great care. It happens with a great amount of discussion and consideration. Maybe there are better solutions than a setting. Who does a feature benefit and who does it not, that a setting makes sense?
Anyways, onto the specific points you’ve mentioned:
I don’t think there is that much of a viable point for this anymore.
There are basically two kind of apps who may want to be launched at startup.
The first are apps which have an specific process that should be started at launch. Think of an mail client that starts at launch to check for mails in the background.
For these apps, we already have the systems in place with the background portal which can be used. This doesn’t need an arbitrary setting in the control center.
The second are apps which the user often uses and wants to keep open between reboots, etc.
In my view, this case is better served by a session restore feature, rather than startup setting in the control center.
And this is currently added to GNOME.
So, for most cases, this is better solved by other systems rather than a setting.
And when the user really needs to tweak it manually, it makes more sense in a tool like Tweaks or Ignition than being placed in the control center.
Fonts basically fall under the same category as themes in this regard. As changing them can fundamentally change the design of the app and lead to unexpected changes to the UI, I don’t see it making its way into the control center.
Similar things are true for window controls.
Just from a design perspective it doesn’t really makes sense to add a minimize button to a default GNOME desktop for example, without a taskbar to minimize to. And if it needs an extension to make sense you already leave the territory for making the case for it to be an official setting in my opinion.
But also: As the one who designed the widget for changing this setting in Refine, I can tell you that from the technical details this setting has the potential for quite a few edge cases which would make it very annoying if you’d wanted to make it an official setting in the control center.
In general: Usability problems should just be fixed properly, rather than being allowed to be tweaked to be not an issue.
I mean, in some cases it may make sense. And there have been a few settings which made their way to the control center because of usability reasons. But that needs in general a more detailed discussion.