I regard this as rather ugly hack, I think this should be somewhere in the settings
Over-riding a theme's pre-configured CSS is not an ugly hack. The theme has a style.css file full of CSS code. You're just adding some to over-ride what's already there.
All themes have standard colors pre-configured in the style.css file. When you use the Customizer to change colours, you are over-riding those pre-configured colours exactly as you over-ride them with "Additional CSS" ... or another style.css in a child theme.
Otherwise it makes no sense to change some colors in the settings and other ones directly in a CSS.
As I explained above ... it's completely normal and does make sense. There are many established themes with premade child themesLike Davinci for Woo) that use a style.css file to over-ride the mother theme's CSS. If you wanted "every" colour, size, border, padding, alignment, font-size etc available to be changed via the Customizer ... it would be HUGE. Customizers just include basic changes that suit most people. If you want more ... add more yourself via Additional CSS or a Child Theme.
I hope this will be resolved in the future.
There's really nothing to resolve. It's all completely normal. If you want to change colours, you have to over-ride the pre-configured colours via the Customizer, the Additional CSS or a style.css in a Child theme. All three methods do exactly the same thing.
There's is no "ugly hack" involved.