I doubt it. Even just changing the font size causes selection issues (e.g., making markdown headings larger than the regular text). So I imagine changing the visible characters will also throw it off. However, there are packages that display a processed version of the source inline, so maybe check them out. Examples I can think of are
What do you mean? Gutters can be added with the Atom API, though most of it will be configured via TextEditor methods. I know the documentation is lacking, so I recommend playing around with what the different things do, to get a clearer idea before committing to anything. I believe new gutters should appear like the line numbers one, except empty initially.
These gutters will stay aligned with the line they represent (like the line number gutter). For something like an entirely different pane, look at the