Markdown works because one person owns the whole picture. The moment you add a second client, that assumption collapses.
You're not choosing between markdown and a database. You're discovering that markdown was always a database just one held together by a single person's understanding. The moment no single person owns the full picture, markdown stops being a feature and starts being a liability.
The answer to your questions database for isolation and access control, markdown for the human-readable layer that people actually need to read and edit. Keep the legibility. Drop the illusion that legibility scales.