When it comes to game servers, especially for highly modified games like minecraft, there's the client facing side, including how the game behaves, and then there's the server administration side.

If I were to interpret the statement made here I would assume that not-a-drop-in while being vanilla compliant means things like:

* It won't support server side mods without you re-writing them in rust

* It won't support bukkit plugins without you re-writing them in rust

* It doesn't support the configuration file format that the java server uses

* Maybe it doesn't support the world file format (which would be server side only)

* Maybe it doesn't support the same administrative commands (which you would only see as an administrator)

etc.

So it can definitely be compatible from the client perspective while being woefully incompatible with any prior experience anyone running a minecraft server might have.