RuntimeTransformHandle.cs line 143 should use handleCamera, not Camera.main (when using two stacked cameras, the camera may need to be set to the second one. Changing this fixes an issue with a strange offset to the raycast when set to Camera.main instead of the proper camera to raycast from)
Also, please add a serializable Layer field for the runtime-created gizmos. Currently the layer has to be set recursively after runtime instantiation in a rather hacky way to get them to be visible with multiple Camera layer-based culling.
With these two fixed, working great for me.