Essentials shows the Kanto Dex by default, with the Johto and National Dexes needing to be unlocked. If the player obtains a Treecko, it will still be recorded in the Pokédex, but won't be accessible straight away because it doesn't appear in the Kanto Dex.
With too many question about National Dex (and I agree that this appears to be a bug), in default Essentials make the National Dex avaliable when erasing all the Regional Numbers OR when the Reginal Dex won't have a name (put also a explanation in settings).
Also make a message in sample event when the player picks the pokédex like: "Kanto Dex avaliable if you have Reginal Numbers, to displays National Dex in start erase the Regional Dex names." or make a National Dex sample event.