In case anyone wants to know what each specific color does, I've looked through the site and identified some uses for each color. It started as just the strange obscure-seeming ones, but I checked through pretty much all of them. I checked against Firefox and Edge, didn't do Chrome and mobile because I was kinda lazy. So no one else has to go through that pain:
- text color: this text goes on for miles (everywhere minus links)
- main background: can you guess what this one is...?
- translucency
- l1: used on background on title pages towards the top (most visible right under the title and pic, makes a nice gradient)
- each seems to be more transparent than the previous one (all the way up to fully transparent)
- couldn't find any obvious uses of l2 through l4
- accent: used for menus, boxes, and the search bar as the background color
- accent l1-l5: used stuff drawn on top of accent boxes mostly
- l1 is used for the background of the image loading buttons and between different scanlations of the same chapter and some accent button hovers?!?!
- l2 is used for the background of the horizontal progress bar during reading (after it's already been loaded) and the Ctrl + K hint on the search bar
- l3 is used for the progress bar during loading (I think?)
- didn't see any obvious uses for l4 or l5
- hover is for when mouse is on top of the button (usually lighter than base in dark mode)
- active is when the button is being clicked (usually darker than base in dark mode)
- mid-tone: didn't find an obvious use in the pages I scrolled, probably should be similar to the text color though
- scrollbar colors: for the vertical scrollbar (does notaffect the horizontal progress bars)
- doesn't work in Firefox (imagine my surprise when I tried it in Edge and actually saw a change...), but does in Edge and (presumably) Chrome
- button accent: main button color and is also used in some borderless buttons on hover (notably on the left sidebar on the home page)
- button accent (alt.): didn't find an obvious use but it should be another button color probably
- primary: this is the main color used in anything that needs to stand out (the Mangadex orange by default)
- used in important buttons, page dividers, links (both in site and cross site), for button hover for cross-site pages (on series pages)
- primary l1: used for very few primary color buttons on hover (most notably, for the current page on the navigation sidebar)
- primary l2: couldn't find any obvious uses for it (theoretically should be the button click color for primary color buttons but...)
- status colors: for publication statuses per series (green for ongoing, blue for completed, etc)
- blue status is also used on the side of chapters that you've already read
- you could change these to whatever you want, but conventions are nice
- indication blue: 404 no obvious uses found
- danger: for "dangerous" buttons, can either be a bordered button for risky actions (like deleting your account) or a borderless button for meh ones (like deleting a chapter you uploaded)
- danger l1 and l2: didn't find anything for these ones either
Anyway, I hope this helps someone while they're designing their themes.