if you import the example skeleton into Blender the transformations are completely wrong (on the right), I straightened them out (left) and added a bunch of constraints. However reimporting the “correct” version into UE4 always messes up the animations, even when using the (old / non rig) retargeting system.
As for compatibility: With the new system you can take the animations created in Blender and recalculate them to fit the default skeleton. Animations created with this rig will not directly work with asset store animations or vice versa, but once you have retargeted them it should not be any problem to interchange them between characters.
The IK targets are purely for the animators and do not have any relevance inside of UE4 (as far as I can tell), they won’t port over, but I don’t think they are needed anyway. If they indeed are necessary I could add dummies, though.