I noticed this issue has been fixed in the 5.0 Release
Edit: My mistake. I had changed my configs and updated to 5.0. I was seeing the stencil draw and able to use it in my post process, and I assumed the issue had been fixed. However upon revisiting, it no longer worked. I believe that the nanite meshes were just not rendering with nanite. Likely due to some config I had been playing with.