How To Reproduce:
1) Setup a new project using LWRP 5.0 (package manager) or LWRP 5.1.0 (latest github as of 11/19/2018)
2) Create a material using the LWRP/Lit shader with Alpha Blending mode and adjust the Albedo alpha to be fairly low.
3) Enable XR in Project Settings, add Oculus or Mock HMD, and set stereo rendering mode to Single Pass.
4) Apply the material to an object in the scene.
5) Set the Clear Flags of the main camera to be Solid Color.
6) Run and notice that the transparent object is not drawn.
7) Set the Clear Flags of the main camera to be Skybox.
8) Set the Skybox Material to 'none' in the Lighting window.
9) Run and notice that the transparent object is not drawn.

Expected Results: Transparent objects are drawn when using clear flags other than skybox and when the skybox material is set to 'none'.
Actual Results: Transparent objects are not drawn when using Solid clear flag or when the skybox material is set to 'none'.

Reproducible in LWRP 5.0.0 and 5.1.0

Tested with Rift using the Oculus SDK and Mock HMD.

Notes:
-Does not affect non-stereo cameras.
-GameView is correct in Editor while the Editor is not playing.
-Also affect rendering of canvas ui elements.