Running a plain vanilla project in Unity 2020.3.0f1 with URP version 10.3.2. I created a simple gradient shader in shadergraph and set it as the skybox material in the example scene.
Have you found a fix? I’ve been running into this as well and been having a difficult time finding a solution, this is one of the first threads I’ve come across that’s a 100% replica of my issue.
Switching Stereo Rendering Mode to Multi-pass under XR Plug-in Management > OpenVR seems to work like you noted. Though this shouldn’t have to be the only solution, as Single Pass Instanced is much more performant.
Edit: Found another thread with a similar problem. HLSL (or ShaderGraph) Skybox Shader with Single Pass Instancing looks like your skybox shader is zclipping due to incorrect scaling while using single pass instancing, disabling zclipping for your skybox shader should fix it (it did in my case). I hope this gets fixed in a future release of URP
If shadergraph has zwrite/ztest options you can change it there. If it does not, you can always export it as a .shader file and add them in yourself. Look up the unity docs for ztest and zwrite, its easy to add in.