Depending on what the scale is on this image from the QR reader section of the Pokemon website, it looks like Pokemon might not all inhabit the same grass on a route.

This image was labeled as being Pikachu's habitat, identified by the Rotom Pokedex once Pikachu's QR code has been scanned. It might just be that it's the only spot a specific Pokemon of a species can be found in once scanned (if they're special give away Pokemon or something similar). But the way it's phrased on the site, especially with you checking the Pokedex for its habitat, makes it seem like it's just letting you register a Pokemon to your Pokedex as seen through a new method. Especially since players can share QR codes from their Pokedex with other players