The problem with separating avians from non-avians comes when they bisect within the same family. We could say "theropod" as the species and in the description of it describe them as ground-dwelling dinosaurs, but that would exclude, like you said, archaeopteryx, as well as even a few species of raptors that are flight-capable, such as microraptor. Since, obviously, microraptor is still a theropod and would fit in with the original "raptor" description this wouldn't work. Archaeopteryx and microraptors were strange little outliers to the general order of things, though, and I think that saying "Dinosaur" as a species would still easily cover them since they fit right into that description anyway.
However, I think what you may be trying to get at is that pterosaurs are definitely very different from what we're trying to describe here, but pterosaurs aren't even dinosaurs, so they shouldn't be included anyway, and if someone wants to play as a pterosaur character they should have a separate species altogether. This is getting off topic, though.
My point still stands that I think saying "raptor" as a species and then, in the description, saying that "raptor" describes all theropods is very misleading and just downright odd. The best way to rework this into a species that makes sense would be to broaden it to "Dinosaur" which would also solve the problem of people wanting to play as non-theropod dinosaurs who would not have an accurate species name. Logistics of avian dinosaurs aside, they're still technically dinosaurs so fitting them into that species wouldn't be a problem. There will always be problems with inclusion, but you can get away with a lot of miscategorizing since a lot of people use "dinosaur" as an umbrella term for pterosaurs and a lot of aquatic species during the time period anyway. If people are searching for any character before the K-Pg extinction, basically, "dinosaur" is probably how they'll phrase it, whether or not it was actually a dinosaur (such as pterosaurs, mosasaurus, plesiosaurs, etc).