It refers to Darwinian evolution, of one specie slowly changing over long periods of time to become another specie, rather than Pokemon evolution where certain conditions are met and one Pokemon immediately becomes another.
To elaborate, consider the wolf. Their encounters with early humans provided a new opportunity for different skill sets among individual wolves to survive and thrive in a way that they previously could not. Their less aggressive, more endearing qualities made them less successful hunters, but much better scavengers from human scraps. This gradually led to their acceptance by humans, but also isolated their gene pool from that of the wild wolves. These "friendlier" versions of wolf genes eventually led to the domesticated dog. Of which, there are now a staggering number of specific varieties, all selectively bred to focus and accentuate certain features present in the dog, while simultaneously diminishing others.
This is the process that Diancie's Pokedex entry is referring to when it says "evolution" in that context. Hundreds to thousands of years in Pokearth's future, all Carbink may eventually be capable of evolving into Diancie. Or, perhaps Carbink will develop a gender ratio, rather than being genderless, and only the females will evolve into Diancies. Events and changes to the environment of Carbink will act on the population over a prolonged period of time to produce a change in the species.
This would also fit a pattern that has been heavily evident in recent Pokemon titles. GameFreak seems to be very intent on making Pokearth feel more real and alive. Part of that involves the slow but inevitable march of change, like this Pokedex reference. Another part is the more in-depth development of ecosystems and predator/prey interactions between different species of Pokemon, such as between Corsola (prey) and Mareanie/Toxapex (predator).
