The following patch solves the issue but it is always clearing the stencil buffer before rendering Noesis onscreen. We should expose a property in the view to control this.

Index: NoesisRenderer.cs

--- NoesisRenderer.cs (revision 14351)
+++ NoesisRenderer.cs (working copy)
@@ -78,6 +78,8 @@
/// </summary>
public static void RenderOnscreen(Noesis.View view, bool flipY, UnityEngine.Rendering.CommandBuffer commands, bool invalidate)
{

• commands.ClearRenderTarget(UnityEngine.Rendering.RTClearFlags.Stencil, UnityEngine.Color.black, 1.0f, 0);

•  FixCommandBuffer(commands);
  
   var eventId = flipY ? EventId.RenderOnscreenFlipY : EventId.RenderOnscreen;

In 3.2.5 we have added an experimental flag to the View (Clear Stencil Buffer) for this purpose.

Thanks for your feedback!