Yes currently thats required for the root export scene. Plans are to remove that requirement.
Actually you can reference any other scene in your project (as a SceneAsset in one of your components) and it will be exported as a gltf (and you can deserialize as a AssetReference in typescript and load it from there)
There is a small sample in the https://docs.needle.tools repository and its how we built out website (all scenes on the website are separate unity scenes and loaded on the fly)
Ok. So theoretically I can take that approach and add a new scene with the required needle setup and reference the existing scene in that configuration to start adding web support with needle without too much other conflict
Cool. Going to play around with this early next week and document any pain points and then reply back to this thread so we can make improvements to that workflow.