What gets extracted from each GitHub surface
Repo home (github.com/owner/repo): the rendered README only — no file tree, no language bar, no contributor row. The output is what you'd get if the maintainer had emailed you their README.md. Wiki pages (/wiki/PageName): the page body with its headings and links rewritten to relative paths so the wiki archive browses offline. Issues and pull requests: the title becomes # H1, the body of the OP becomes the content, comments become sub-sections with author and timestamp attribution. Discussions: same shape as issues, with the accepted answer marked when present.
Why convert what's "already Markdown"
READMEs are Markdown in the source repo, but the page you visit at github.com/owner/repo is HTML rendered by GitHub's own renderer. Copy-pasting that rendered HTML brings emoji shortcuts as Unicode glyphs, task-list checkboxes as <input> elements, and admonition syntax as styled divs — none of which round-trip to plain Markdown cleanly. Hitting "Raw" gives you the source but loses GitHub's rendered improvements (resolved relative links, embedded images, expanded shortcodes). The converter splits the difference: the rendered output, normalised back to clean GFM. If the repo's real docs are stored as PDFs in the repo, also try PDF to Markdown.