Personally I am not a developer, so my answer may not be 100% accurate.
So Thrive is a game that wants to do what Spore didn't do, and two major factors of that is scientific accuracy and freedom. A lot of animals in real life have exoskeletons (carbs, oysters, maybe even shrimp). So I think there will defiantly be an option to have an exoskeleton or endoskeleton. To have both sets of skeletons will probably also be possible.
My preferred approach is to simply make tissue around the surface hard calcium carbonate. Of course, it will limit my growth and movement, so I might want to make it sheddable. If I'm not into the full exoskeleton deal, I'll make a more snakeskin-like material.