After the last update, it seems that the settings to exclude some planets stopped working.
As in either you can have the custom better planets FOR ALL, or you can have the new setup while not being allowed to alter it at all. Don't know why, don't know how but I'd like the new setup while being allowed to change it a bit.

(So turn on the custom parameters and turn off all the "Nauvis" which is meant to use the basic zones and it uses the really basic instead of the update ones)

So what's the issue?
You can disable planet's independently.
Each planet has defaults (taken from the mod) and master switches to enable/disable different features

Yes but it doesn't work now since there are 2 stages you can have

There is the updated one, the newest layout
There is the natural layout

Now you can modify the natural layout but you can't the update one. So if you choose the update one and have a planet that just feels off like it should be somewhere else, you can't move it since the override is disabled if you choose the newest update layout

I just wish there was a way to make the updated layout the basic one which then can be further edited which at this moment is not a possibility

Sorry I really didn't understand what you are talking about.
Can you describe step by step what do you want to achieve and in what ways mod prevented you to do this?

If you turn off every single Override this planets coordinates button but turn on the override the layout that was added in the last update, you get a completely different state of the map than if you turn on the new updated layout.

But if you have the new updated layout, you can't configure it and there is no easy way to make something similar to the updated layout because you can't change planet coordinates if you use the update layout.

This would be so much easier with like paint so if this is still not understandable, then I'll just show you what I mean in some way