You can't go back to MeshFusion once you commit but you CAN still continue to model with the mesh it produces - If Groboto is any indication, the resulting mesh will have decent topology and should be easy-ish to work with.

However, the same is true of MoI ... once you do your boolean operation, you can't go back and change your mind. If you want to do something different, you have to rebuild the surfaces and try again. Right?