If only I can help with FBX animation, but I surrender using FBX for animated mesh file long time ago since XNA time. Just like what your planning to do, I wrote my loader/parser for mesh file type I supported.
Basically I’m just using Monogame as a renderer after porting my engine in XNA, I don’t use Model class and I don’t use content Pipeline to cook the Model mesh in short I have my own MeshContent and ModelEntity class so I’m not limited to MG Model.Draw() and what should be embedded ot not to model mesh.
But I think MG team and XNA team did a great job for creating Pipeline Tools, for other developers to extend it, we know that even in XNA we have to write our own processor/write for model animation.
Good luck dude ^_^y