This topic is relevant to me. I've been doing some homebrew D&D (3.5 SRD, because free) based on Geneforge with my friends in real life. Though I've encouraged them to play the games, they haven't yet, and have gotten in the habit of calling our game "the Petri dish world." In my game, yes, there are unshaped animals and plants, but they're not common in any areas that have any connections to Shapers because the Shaped-things are so much more efficient at what they do. Where there are chickens roaming a non-Shaper community, there are probably chicken-like things that produce a dozen eggs a day and aren't as territorial or hierarchical. Or perhaps more territorial, if there's danger of wild animals trying to eat them. (I've owned chickens, and have seen just how vicious they can be with a snake.) But in communities far from Shaper influence, or in wilderness areas Shapers haven't decided to mess with yet, more natural creatures and plants will be present.
Shapers aren't stupid; they know that over the course of a few million years, most things evolved quite well to fill specific niches on their own, and they wouldn't be interested in doing much more than tweaking stuff that already worked. It's the specialty stuff that a Shaper wants to design, stuff that only matters to humans and human society, like livestock and warfare. But if they want to make a desert a forest, or a siege weapon that can move around on its own and follow orders, they don't want to wait around a few eons for evolution to make that happen on its own.
In making my D&D game, I know they're lizards, but fyoras seem most balanced when I've used the stats for various kinds of cats (ranging from housecat to dire tiger, depending on the party level), and just tack on a spit attack of varying intensity. (I nearly wiped a level 1 party with just the housecat variety, because I gave them a 1d4 spit they could use every turn. I've since learned to scale it.) Cats seemed like a good template because the fyoras seem to hunt and think like cats when rogue. Also, cats have a good Dexterity, so they are fairly accurate with the spit.
In making stats for the shaped things, I've found it easiest to start with how the creation thinks, and then add or take away things from other animals based on that. Which I figure is similar to how Shapers design a new creation: look at normal animals and plants, and add things you want from other life until you've got a mix that makes you happy and doesn't immediately die. Most creation's special abilities can be borrowed from elsewhere in nature, many with only minor tweaks: bombardier beetles with their explosive spray, archer fish spitting water at bugs, porcupine quills, etc. Put a bombardier beetle's explosive glands behind a llama's spitting muscles, and slap that overpowered mouth arsenal on a lizard or a wolf, and bam, fyoras and roamers. Which would also be how you get things like unstable roamers, since I wouldn't be surprised if that whole bombardier beetle thing was tricky to get right. And once you got one design stable, there's no reason not to build on it, like the glow-in-the-dark roamer in G5. As far as magic creations go, it would just be a matter of adding in whatever gland or brain chemical or whatever makes magic happen.
And given the arrogance of Shapers, I have no doubt that if a Shaper ever discovered dinosaur fossils, their first thought would be "I bet I could do that" and not "I should painstakingly study this to find out what life was like several million years ago."