hmm I only have experience with blender so thats what I can comment on but you can use shape keys to create some more gradual inbetweens but ya as far as I can tell making seperate models for different phases is kind of unavoidable. If it were me I'd use some combination of lighting shaders and vfx to obscure the details and only worry about the silhouette of the character for inbetweens. Use shape keys were I want it to look more slow and gradual and a different model when the more drastic changes occur in the transformation.
Anyway, big fan of your work! Good luck with the launch! I'm looking forward to playing Orc Bastion :)