3 - I noticed that after tweaking some visibility options in all panels eg. 3d viewport, outliner…etc if those panels are closed and open again they go back to the default look. is there a way to store the changes?
Yes, under User Preferences → Theme → 3d Viewport → Theme Space → Header, you have to change the alpha value.
No (afaik), but that should be easy to implement.
Not sure about what you mean here.
If what you want is to have those tweaks every time you open a new file, then you have to go to File → Defaults → Save Startup File Notice that it’s saved as a regular .blend file, so it will include every change you made, including objects, angle of view, ecc… so be aware of it
If instead what you mean is that when you close an editor and then open a new one of the same type (as an example joining properties to the outliner and then opening a new outliner) the settings are restored, then that’s normal and there’s really nothing you could do about it.
yes that’s what I meant - perhaps it would be nice to see that implemented in the future, having an option in the preferences would be quite useful since lots of people don’t use the top tabs (spaces) but they add and remove panels on the go.