The inline CSS and the style.css don’t load the same values – there’s a small percentage of CSS you can find in both, but it’s slowly being removed from the style.css file.
The inline CSS come from PHP code which grabs the CSS values from the database/defaults – this is beneficial because it allows child themes to be created which can edited using the Customizer.
If you try and change the .inside-header padding in the Simple CSS plugin, it will work because it’s loaded below the other CSS. The style.css file is loaded above the inline CSS, so the inline CSS is taken as more important (which it is).
The values that are changeable in the Customizer require some of the add-ons – for example the Spacing add-on.
When it comes down to it, this is the most efficient, customizable way to print the CSS. It makes the theme much more powerful and allows for easy child theme creation.