The app looks great and there are several reasons why I would want full CSS control:
Fix minor UI inconsistencies (rather than bother you with them). Sometimes, things are not pixel perfect or even confusing (dragging an email into a todo list).
Personalized theme. I want to experiment with different alignments, tags, etc. This requires using multiple classes/selectors/pseudoelements in the CSS declarations — which get ignored/removed.
Productivity in experimenting with UI changes. Now the CSS gets reformatted and the editor is very clumsy (especially with indentation).
So, as a solution, I’d rather see one CSS (which can be reset to your default), fully customizable (loaded AFTER the default CSS, as a “theme”). Splitting the custom CSS in two (color/layout) is also somehow confusing for someone who uses CSS, because of having to change in two places if you want to customize a single UI component.
Happy to jump on a call for more details—I don’t know what I can record as a relevant video).