I finally got our project to run with Multiplayer Play Mode, but encountered a bug after updating the project (e.g., code/scene change).
Virtual Player spams exceptions like NullReferenceException. As I checked, some components got missing assets in VP scene.

Reactivating VP solves the issue.
Used Unity 6000.0.26f1 with com.unity.multiplayer.playmode 1.3.1
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Strange, I tried MPPM in 2 Bitesize samples to report a bug:
And couldn’t reproduce the same issue =(
Tried disabling Domain and Scene Reload like in our project. Still no issues.
Tried upgrading to Unity 6000.0.28f1, didn’t help
Tried upgrading to com.unity.multiplayer.playmode 1.3.2, didn’t help
Still having the issue of missing asset references in VP scene
Looks like it was finally fixed. I installed Alpha (6000.2.0a6) and could finally use MPPM without any issues.
Used MPPM v1.4.0, but upgrading only MPPM version doesn’t help. I tried the same version in LTS (6000.0.36f1) and still couldn’t use it without issues.