@Eiji Great observation 
Yes, the parsing library from Surface itself (which SurfaceFormatter uses under the hood) does not expose those comments, so we lose them. However, you can replace them with interpolated Elixir comments instead.
{{ # Some comment }}
I think it would be great to be able to keep HTML comments. If there is enough interest, perhaps the Surface parser can be modified to expose them.
In the meantime, I have added a more thorough explanation in that section of the docs to hopefully make the “why” more clear: https://hexdocs.pm/surface_formatter/Surface.Code.html#format_string!/2-html-comments
