Actually, there is a difference, but that’s probably not related to the Markdown parser itself but rather to Nextcloud’s Markdown file autocorruption feature.
This:
This is [a `geo:` link](geo:0,0?z=15 "That's where the Equator intersects Greenwich").
Gets changed by the Nextcloud frontend to this, which is not at all the same thing:
This is [a ](geo:0,0?z=15 "That's where the Equator intersects Greenwich")`geo:`[ link](geo:0,0?z=15 "That's where the Equator intersects Greenwich").
…and that’s even though the Markdown is not open for editing in the first place. Let’s just say that Markdown handling on the frontend is not exactly robust, though that’s a separate issue.