So what exactly do I have to hack to make this happen?
Had to remove .cm-s-THEMENAME from theme, put !important to any rule and save wrapped by @-moz-document regexp(".*") {} to userContent.css (Firefox). Noice.
Would still be cool to overwrite setting like indentation and gutter-order as well.
It doesn’t have to be wrapped by @-moz-document regexp(".*") {} to be valid on any site of course.