[[title]] tag returns the first line of the draft. It does not make any changes to it, or process it in any way - just returns the first line. So that is expected behavior.
Running it through Markdown would not get you results you need. That converts to HTML and you’d end up with HTML tags in the note name - which is also undesirable.
If you are using the first line as a title, I would recommend just not including the header markings. You could, alternately, use the
[[safe_title]] tag. It creates a file-name safe version of the first line. That would strip the ###, but depending on the title you want, may or may not be what you want because it strips other non-file name safe characters.
There are other ways to clean a title using scripts if it needs further customization, but generally speaking I would just suggest putting in the the first line the way you want the note named, then use [[body]] instead of [[draft]] in the note template to not include that note title in the note itself to prevent duplication.