I was happy when you introduced the Layouts CSS menu because it made a lot of things easier. However, the more I used it, the more I realized that it has a problem.
When you write your CSS into Layouts CSS, the site first loads everything on the style.css file, and THEN it loads the layouts css. This means that for a short time (which depends on your internet and computer speed) hidden radiobutton icons can appear before your menu is formatted, anchor texts can appear in their original blue format before they receive their final appearance, etc.
Moving all your CSS from Layouts CSS into the style.css file in Appearance/Editor removes these issues, so I would advise to use that instead.
I am not entirely sure we can or should be modifying the theme styles.css file, but I see your point about the loading problem for custom CSS. I am creating a ticket for our Layouts developers about this issue, and they will evaluate and, eventually, improve this on their side.