Indeed this is the balance we tried to find. Agenda is not a markdown editor, the internal format we use is not simple markdown text. We support more advanced features than you can build with pure markdown, and expect to add many more. We also feel that exposing raw markdown can be off-putting to a lot of people that might not be familiar with it. As such we wanted a more classic text editor that shows bold as bold and italic as italic without necessarily showing asterixes and underscores for example, and clickable links without needing to be enclosed in square brackets etc.
Having said all that, we do support using markdown syntax as shortcuts to easily format text and insert checklist items etc, as described in this topic: