I just bumped into the exact same issue while playing around with the meta quest 3 and UE 5.2 and finally found a solution! Maybe it helps someone:
When the layer placement inside the OculusXRPassthroughLayer was set to Overlay, passthrough was working perfectly, but I didn’t see any 3d objects. When I set it to Underlay, I could see my 3d objects, but the passthrough was gone entirely. Setting it to overlay and reducing the alpha, I was able to see both, semi transparent passthrough and 3d objects. Still not what we want…
Now, all this was with an unreal project that I created from scratch, using the settings recommended here:
https://developer.oculus.com/documentation/unreal/unreal-passthrough-overview-gs/
Testing was done with a packaged project, installed on the quest 3, not with in-editor testing.
I could however get fully opaque passthrough and 3d objects working, when I used the vr template by epic. So in the end, I compared the rendering settings one by one between the projects and what actually did the trick for me was changing the Mobile Antialiasing Method from “None” to "Multisample Anti-Aliasing (MSAA) in the new project. With that, “Underlay” works as expected.