I ran into the same issue, NGO not respecting the wantsToQuit choice. I ended up making a fork and commenting out OnApplicationQuit in NetworkManager.cs for the specific version I'm using.

https://github.com/Unity-Technologies/com.unity.netcode.gameobjects/blob/develop/com.unity.netcode.gameobjects/Runtime/Core/NetworkManager.cs#L1304

this seems to have done the trick. Note that I don't know yet if this has any adverse effects when actually quitting.