Great suggestion about being able to upload a file, but what you might want to do is create your own Style Preset based off one of my defaults such as Modern Moodle and then drop in your code at the bottom.
Another idea is you could use the Custom SCSS textbox to at the bottom of the colors page to add in your custom styles for sections, etc.. They will be stored in the database and will carry over when you update the theme.
Between these two options you should be able to customize the look of your site without hacking the theme.
As for any render overrides you'd have to copy/paste that into the theme with each upgrade.