Hi there,
WordPress stores the Additional CSS data as a “theme_mod”, so it’s attached to the theme you’re using.
If you switch themes, the CSS will go with it. However, it should come back once you re-activate the theme.
I don’t agree with it on their part, but that’s the route they took.
The site logo acts the same way.
The rest of your layout (Customizer settings) are stored as regular options, so switching/deactivating themes shouldn’t affect them at all.