A test for this is to have the HoloPlay Capture set to clear depth only, and a 2D camera also in the scene rendering different layers, also set to depth only. When you change the depths of the cameras, they should swap which is drawing over which -- currently, that doesn't work as the HoloPlay Capture doesn't ever draw over the 2D camera.
Additionally, the clearing flag names are atypical.
"My second camera (non-Holo), call it BackgroundCam, has a depth of -10 and contains 3D objects. It is set to clear Skybox. The Holo camera has a depth of 10 so that it draws over the second camera. The Holo camera, I've tried clearing to None and Depth, but both are inconsistent in whether I'll actually see the results from BackgroundCam. I am trying to avoid using a Quad to the scene. I should point out I am using v1.2.x of the Holo plugin."
"I see, so the inverse of what I was doing. You want the HoloPlay Capture to draw over a 2D camera's render. I can try that."
"The background cam is a 3D cam pointing at some objects way off in the distance."
"Yeah I've seen the issue now @ooCHUMoo - in my opinion, the test for this is to set both camera's to only clear depth - the HoloPlay Capture and the 2D camera - and then ensure that when you flip depth one way or another, it behaves as two 2D cameras would in the same scene."