Let's say Pokemon Q is catchable on Route 9. If there is a bush, and some red flowers (these seem to act like normal grass) will Pokemon Q only be catchable in one of the two, or can they be caught anywhere on the route?
There can be certain types of Pokemon that are only available in flowers in Generation VI. For example, Bulbapedia lists some Pokemon that can only be caught in the yellow flowers on Route 16.
There are also taller grass patches which may have different pokemon than regular grass in generation IV onwards.
However, patches of the same type within the same route will always have the same Pokemon as each other. One patch of normal grass in a route will have the same pokemon as a disconnected patch of normal grass for example.
From my searching, only two routes have examples of this:
Route 16 - No Pumpkaboo in Yellow Flowers Route 22 - Diggersby, Azumarill, and Bibarel in Yellow Flowers, Bunnelby, Azurill, and Bidoor else
I have found on other routes, however, examples of changed rarities.
For example, on Route 12, Miltank is more common in one kind than others.
Edit: Somehow my tablet removed this, but forms of Flabebe are also affected by certain flower beds. And on the swampy routes, some Pokémon, such as Weepinbell, cannot be found when walking through the shallow water.