Thanks! Yep you can create either provide your own %Autumn.Theme{} or modify existing ones, for example:
%{highlights: highlights} = theme = Autumn.Theme.get("github_dark")
red_text_style = %Autumn.Theme.Style{fg: "red"}
highlights = Map.put(highlights, "string", red_text_style)
theme = Map.put(theme, :highlights, highlights)
Then format using that theme:
MDEx.to_html!("""
```elixir
String.upcase("elixir")
```
""",
syntax_highlight: [formatter: {:html_inline, theme: theme}])
You’ll see <span style="color: red;">"elixir"</span> in the output.
I should probably implement the Access behaviour to let you just call put_in(theme, [...], value) 
EDIT: Autumn is another library, you can find docs at Autumn — Autumn v0.7.0
