You can upload your own CSS files to a directory of your server to make them available as themes: https://join-lemmy.org/docs/administration/theming.html
Additionally, lemmy-ui has a flag called LEMMY_UI_CUSTOM_HTML_HEADER which I assume allows you to add a JS script to be executed on page load, which you could use to modify the HTML after the fact.
To modify the HTML in a more proper way, you'd have to pull the lemmy-ui project (https://github.com/LemmyNet/lemmy-ui), make your changes and then build your own docker container with it.