I forgot to mention that markup.goldmark.renderer.unsafe is already set to true. I edited my post about it.
Like you said, shortcode using % should render markdown content in it. And since there is another shortcode using < so it will also get rendered. But somehow, shortcode using < isn’t correctly rendered.
I also removed more indentation in my shortcode code, and it partially recovered layout part. I suspect indentation is the problem.
It turned out that another dependency that my shortcode was using has indentation, and it made rendered shortcode become code block.
I copied those dependencies and removed indentation, and now it renders correctly.
Thank you for the help!