After asking this question: http://community.monogame.net/t/2d-transformations-hierarchy-like-with-bones-with-matrix/8679 I ended up implementing my own solution, and I though it may be useful to some of you guys. So I made the following repo:
In short, it implements a Sprite class with basic transformations (position, scale, color, zindex, rotation, etc), which you can put inside another Sprite (or Container) and the transformations will inherit in a way suitable for making 2D bones-based animation. In other words it implements Sprites and Containers that support transformations hierarchy.
For example, if you place an item at the palm of the player and later you rotate or move the entire arm, the item will "stick" to its relative position and always appear at the right place.