Runtimes are open source tought. Why such restriction for used tools?
We want to have it be very moddable by a community. So we want all of the tools we use to be available to them. If we used Spine our animation technique wouldn't be freely available to everyone, with Blender, it is.
I've used Spine before and I do agree that it's wonderful, however it's not open source or free.
This technique also does have some advantages, we can create 3D models of everything, then render them as 2D, which would allow us to easily show them from a different perspective without drawing another Sprite, and it would allow us to easily mix 3D and 2D elements into the same environment.
Modding support make sense. In our up coming game Hardland we also allow modding and we use blender based art pipeline for same reasons.