I definitely will add additional keyboard support in the future thank you for the tip.
Thank you for the debug output. That definitely points to something I was not expecting. But Hopefully it will help me run down the bug.
Per your question. Although I am using threaded loading internally. In reality threaded loading is not possible. This version of Godot is using the Single Threaded Web build of Godot. Though I am pretty sure my Background loading models does print that it is using a thread. In reality the code detects it is a web build and knows it cannot use a thread. I need to modify that print statement as it is misleading. Though, on a desktop version it would use threads. So unfortunately any loading is actually done on the main thread and will cause stuttering. I do think I could have loaded the entirety of the ship in a single scene. But I still need to test that theory and see if it holds for a phone, as I am hoping to also target smart phones. Another thing I would like to try in the near future is to get scenes to be sufficiently chunked by making many sub scenes and then see if I can load the dependencies first at a rate of 1 dependency per frame, as that may let me do some preloading and simulate it being a background thread. Definitely more work to be done in that area.